CHANGELOG.md

# nf-core/sarek: Changelog

All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [3.10.0](https://github.com/nf-core/sarek/releases/tag/3.10.0) - Aktse

Aktse is a mountain hut on the northern shore of Laitaure, on the Kungsleden trail at the edge of Sarek National Park.

### Added

- [#2176](https://github.com/nf-core/sarek/pull/2176) - Add Parabricks HaplotypeCaller as GPU-accelerated germline variant caller (`--tools parabricks_haplotypecaller`)
- [#2208](https://github.com/nf-core/sarek/pull/2208) - Add varlociraptor/filterfdr

### Changed

- [#2208](https://github.com/nf-core/sarek/pull/2208) - Update somatic freebayes params (remove `--pooled-discrete` and change `--min-alternate-fraction` from 0.03 to 0.01), move chunk_size param
- [#2210](https://github.com/nf-core/sarek/pull/2210) - Update bcftools to 1.23.1
- [#2229](https://github.com/nf-core/sarek/pull/2229) - Update EnsemblVEP to 116.0
- [#2232](https://github.com/nf-core/sarek/pull/2232) - Migrate local code to the lowercase `channel` factory for Nextflow strict-syntax / 26.x readiness
- [#2235](https://github.com/nf-core/sarek/pull/2235) - Nextflow strict-syntax / 26.x readiness for local code: explicit, named closure parameters (replacing implicit/generic `it`), `_`-prefixed unused parameters, and removal of unused `take:` inputs. Previously-dropped Manta candidate VCFs and Sentieon gVCF indices are now emitted.
- [#2235](https://github.com/nf-core/sarek/pull/2235) - germline CNVKIT reuses the shared `CRAM_TO_BAM` conversion instead of re-converting CRAM internally, avoiding a duplicate conversion. Side effect: with `--step variant_calling` (user-supplied CRAM/BAM), CNVKit output files are named after the input file rather than the sample; runs from FASTQ are unaffected.
- [#2238](https://github.com/nf-core/sarek/pull/2238), [#2239](https://github.com/nf-core/sarek/pull/2239), [#2240](https://github.com/nf-core/sarek/pull/2240), [#2241](https://github.com/nf-core/sarek/pull/2241), [#2242](https://github.com/nf-core/sarek/pull/2242), [#2243](https://github.com/nf-core/sarek/pull/2243), [#2244](https://github.com/nf-core/sarek/pull/2244) - Migrate all modules to use topic channels (bumps gatk4spark 4.6.1.0 → 4.6.2.0, fastp 0.24.0 → 1.1.0)
- [#2252](https://github.com/nf-core/sarek/pull/2252) - Update `bbmap/bbsplit`, `gatk4/applybqsr`, `parabricks/fq2bam` (4.6.0 → 4.7.1), `rbt/vcfsplit`, `sentieon/*`, `snpsift/annmem`+`annmemcreate` (5.4.0a → 5.4.0c), and `yte` modules to their latest revisions. Side effect: `GATK4_APPLYBQSR`'s bam/cram output format is now set directly via a `params.save_output_as_bam` process argument rather than `ext.suffix`, so a custom `modules.config` override of `ext.suffix` on `GATK4_APPLYBQSR` no longer has any effect.
- [#2255](https://github.com/nf-core/sarek/pull/2255) - Template update for nf-core/tools v4.1.0. This also collapses the list-form `publishDir` blocks in `conf/modules/*.config` into single maps that route through `saveAs`, required because nf-core/tools 4.1.0 lints via `nextflow config -o json`, which fails on a closure nested inside a collection. Published output layouts are unchanged.
- [#2262](https://github.com/nf-core/sarek/pull/2262) - The `gatk4spark/applybqsr`, `gatk4spark/baserecalibrator` and `gatk4spark/markduplicates` modules now bind-mount the host's `/etc/passwd` and `/etc/group` to work around Spark's `UnixLoginModule` failing to resolve a username for the container's UID, for Docker and Podman only (not Singularity/Apptainer). `GATK4SPARK_APPLYBQSR`'s bam/cram output format is now set via an `output_suffix` process argument rather than `ext.suffix`, so a custom `modules.config` override of `ext.suffix` on `GATK4SPARK_APPLYBQSR` no longer has any effect.

### Fixed

- [#2184](https://github.com/nf-core/sarek/pull/2184) - Skip nf-schema path-existence validation for `snpeff_cache`, `vep_cache` and `igenomes_base` so pipeline launches succeed when the default S3 buckets are not accessible
- [#2216](https://github.com/nf-core/sarek/pull/2216) - Fix `--normalize_vcfs` dropping a real ALT allele of `1/2` multiallelic sites (`bcftools norm --rm-dup all` → `--rm-dup exact`)
- [#2257](https://github.com/nf-core/sarek/pull/2257) - Fix two cases that completed successfully without producing the requested output: `--tools parabricks_haplotypecaller` no longer counts as a joint-germline caller, so requesting `--joint_germline` without one now fails early instead of finishing without any variants; and `--vep_loftee` no longer silently omits `LoF` annotations under `-profile conda`, where the plugin path was hardcoded to `/opt/conda` instead of being resolved from `$CONDA_PREFIX` at runtime
- [#2241](https://github.com/nf-core/sarek/pull/2241) - Bump `mosdepth` (0.3.10 → 0.3.14) so its htslib can decode CRAM 3.1 written by samtools 1.24; the previous container silently produced empty coverage files, dropping the mosdepth MultiQC sections (most visible in the parabricks path)
- [#2264](https://github.com/nf-core/sarek/pull/2264) - Pin merged samtools output to CRAM 3.0 for compatibility with downstream callers, use engine-specific GPU container options for Parabricks HaplotypeCaller tests, and replace the deprecated `cat/cat` module with `find/concatenate` for merged Control-FREEC mpileups

### Removed

### Dependencies - modules

| Dependency    | Old version | New version |
| ------------- | ----------- | ----------- |
| bcftools      | 1.21        | 1.23.1      |
| coreutils     | -           | 9.4         |
| findutils     | -           | 4.6.0       |
| htslib        | 1.21        | 1.24        |
| varlociraptor | 8.9.3       | 8.9.5       |
| ensembl-vep   | 115.2       | 116.0       |
| gatk4         | 4.6.1.0     | 4.6.2.0     |
| gatk4-spark   | 4.6.1.0     | 4.6.2.0     |
| bwa           | 0.7.18      | 0.7.19      |
| bwa-mem2      | 2.2.1       | 2.3         |
| fastp         | 0.24.0      | 1.1.0       |
| fgbio         | 2.4.0       | 3.1.2       |
| gawk          | 5.3.0       | 5.3.1       |
| pigz          | 2.3.4       | 2.8         |
| svdb          | 2.8.2       | 2.8.4       |
| tiddit        | 3.6.1       | 3.9.5       |
| vcftools      | 0.1.16      | 0.1.17      |
| samtools      | 1.21        | 1.24        |
| mosdepth      | 0.3.10      | 0.3.14      |
| cnvkit        | 0.9.11      | 0.9.12      |
| xz            | -           | 5.8.3       |
| parabricks    | 4.6.0-1     | 4.7.1-1     |
| snpsift       | 5.4.0a      | 5.4.0c      |

### Dependencies - plugins

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |

### Parameters

| Params                              | status |
| ----------------------------------- | ------ |
| `--varlociraptor_events_germline`   | New    |
| `--varlociraptor_events_somatic`    | New    |
| `--varlociraptor_events_tumor_only` | New    |
| `--varlociraptor_fdr`               | New    |

| Parameter   | Old default | New default |
| ----------- | ----------- | ----------- |
| vep_version | 115.2-1     | 116.0-0     |

### Developer section

#### Added

- [#2225](https://github.com/nf-core/sarek/pull/2225) - Add contributor ORCIDs to `nextflow.config`
- [#2228](https://github.com/nf-core/sarek/pull/2228) - Add `AGENTS.md` file with nf-core agent instructions

#### Changed

- [#2178](https://github.com/nf-core/sarek/pull/2178) - Template update for nf-core/tools v4.0.2
- [#2225](https://github.com/nf-core/sarek/pull/2225) - Back to dev (3.9.1dev)
- [#2229](https://github.com/nf-core/sarek/pull/2229) - Update nft-utils to 1.0.0, migrate `getAllFilesFromDir` to `getAllFilesFromPath` in test utilities
- [#2233](https://github.com/nf-core/sarek/pull/2233) - Replace the last remaining deprecated `channel.from` with `channel.of` in `prepare_genome`
- [#2234](https://github.com/nf-core/sarek/pull/2234) - Replace deprecated `.set {}` channel terminator with plain assignment in local subworkflows for Nextflow strict-syntax / 26.x readiness
- [#2237](https://github.com/nf-core/sarek/pull/2237) - Update muse/sump module to check if the index is older before touching it

#### Fixed

- [#2229](https://github.com/nf-core/sarek/pull/2229) - Fix LoFTEE test to validate CSQ fields instead of asserting nothing

#### Removed

## [3.9.0](https://github.com/nf-core/sarek/releases/tag/3.9.0) - Sarvesjåhkå

Sarvesjåhkå is the biggest stream from Sarvesvágge to flow in Rapaätno.

### Added

- [#2087](https://github.com/nf-core/sarek/pull/2087) - Add `bam` as output format for parabricks/fq2bam, add multi lane support
- [#2194](https://github.com/nf-core/sarek/pull/2194) - Add `--vep_cache_preflight_check` parameter to force preflight check for local VEP cache download
- [#2199](https://github.com/nf-core/sarek/pull/2199) - Add animated metro map (`docs/images/sarek_subway_animated.svg`) with dots flowing through the workflow

### Changed

- [#2055](https://github.com/nf-core/sarek/pull/2055) - Sort final vcf in varlociraptor sbwfs, update varlociraptor, and add `--force-samples` to the `bcftools merge` of germline/somatic VCFs so the merge proceeds (renaming colliding columns) instead of failing when sample names collide
- [#2141](https://github.com/nf-core/sarek/pull/2141) - Update snpeff
- [#2194](https://github.com/nf-core/sarek/pull/2194) - Replace local `annotation_cache_initialisation` and `download_cache_snpeff_vep` subworkflows with nf-core `utils_annotation_cache` and `cache_download_ensemblvep_snpeff`
- [#2209](https://github.com/nf-core/sarek/pull/2209) - Add flowing dots for the additional `bam/cram` and `vcf` entry points on the core line and the `cram` entry on the germline line in the animated metro map
- [#2220](https://github.com/nf-core/sarek/pull/2220) - Update DeepVariant to `1.10.0` and sync `gatk4/mergevcfs`; both modules now report tool versions via the `versions` topic

### Fixed

- [#2117](https://github.com/nf-core/sarek/pull/2117) - Silent failure with multi-lane samples, including stripping `sample_lane_id` in the UMI consensus `groupKey` so `groupTuple` can merge lanes from the same sample (previously blocked by the retained per-lane `sample_lane_id`)
- [#2143](https://github.com/nf-core/sarek/pull/2143) - Varlociraptor collecting multiple scenario files for one sample
- [#2146](https://github.com/nf-core/sarek/pull/2146) - Fail early when `--no_intervals` is used with joint germline HaplotypeCaller
- [#2147](https://github.com/nf-core/sarek/pull/2147) - Fix empty fastp output folder created when trimmed reads are not saved
- [#2152](https://github.com/nf-core/sarek/pull/2152) - Fix missing `params.` prefix for `umi_tag` in markduplicates config
- [#2154](https://github.com/nf-core/sarek/pull/2154) - Fix `--save_output_as_bam` causing duplicate emission errors, silently skipping variant calling, and running unnecessary CRAM-to-BAM conversions; add BAM output support for the sentieon dedup path; stop publishing converted BAMs when `--save_output_as_bam` is not set; widen the `--use_gatk_spark markduplicates` + `--save_mapped` incompatibility check to error regardless of `--save_output_as_bam`
- [#2189](https://github.com/nf-core/sarek/pull/2189) - Fixes the `interval_name` → `intervals_name` typo in the branch step (was a silent no-op)
- [#2190](https://github.com/nf-core/sarek/pull/2190) - Fix controlfreec crash in edge cases when no breakpoints are found
- [#2196](https://github.com/nf-core/sarek/pull/2196) - Update `vep_version` parameter from `115.0-0` to `115.2-1` and fix `loftee_path` from `/usr/local/share` to `/opt/conda/share` to match the container VEP installation path
- [#2219](https://github.com/nf-core/sarek/pull/2219) - Downgrade `controlfreec/assesssignificance` from `control-freec` 11.6b (`hde5307d_3`) back to 11.6 (`h1b792b2_1`)

### Removed

### Dependencies - modules

| Dependency                   | Old version | New version |
| ---------------------------- | ----------- | ----------- |
| controlfreec                 | 11.6        | 11.6b       |
| deepvariant                  | 1.9.0       | 1.10.0      |
| ensemblvep                   | 115.2       | 115.2       |
| gatk4 (in `GATK4_MERGEVCFS`) | 4.6.1.0     | 4.6.2.0     |
| --htslib                     |             | 1.23.1      |
| multiqc                      | 1.33        | 1.35        |
| sentieon                     | 202503.01   | 202503.02   |
| snpeff                       | 5.3a        | 5.4c        |
| varlociraptor                | 8.7.4       | 8.9.3       |
| yte                          | 1.9.0       | 1.9.4       |

### Dependencies - plugins

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| nf-prov    | 1.2.2       | 1.7.0       |
| nf-schema  | 2.6.1       | 2.7.2       |

### Parameters

| Params                        | status |
| ----------------------------- | ------ |
| `--vep_cache_preflight_check` | New    |

### Developer section

#### Added

#### Changed

- [#2055](https://github.com/nf-core/sarek/pull/2055) - Update varlociraptor to use only one input channel, swap to topics
- [#2087](https://github.com/nf-core/sarek/pull/2087) - Move parabricks config into its own, adhere to strict syntax, swap to topics
- [#2139](https://github.com/nf-core/sarek/pull/2139) - Back to dev (3.9.0dev)
- [#2141](https://github.com/nf-core/sarek/pull/2141) - Update vcf_annotate_snpeff subworkflow, swap tabix/bgziptabix and snpeff to topics, strict syntax
- [#2142](https://github.com/nf-core/sarek/pull/2142) - Replace custom Slack/Teams notifications with nf-slack plugin (v0.5.0) bot token auth, scoped entirely to CI cloud test workflow, Remove Azure cloud test profiles, use dynamic matrix for selective test dispatch, Fix cloud test to use secrets instead of vars for TOWER_BUCKET_AWS, TOWER_COMPUTE_ENV, and TOWER_WORKSPACE_ID
- [#2159](https://github.com/nf-core/sarek/pull/2159) - Fix strict syntax errors
- [#2169](https://github.com/nf-core/sarek/pull/2169) - Prepare release 3.9.0
- [#2170](https://github.com/nf-core/sarek/pull/2170) - Update dependencies
- [#2173](https://github.com/nf-core/sarek/pull/2173) - Update MultiQC
- [#2188](https://github.com/nf-core/sarek/pull/2188) - Update all `sentieon/*` modules to `nf-core/modules@7ad1622c`. Brings in `--interval` honouring in `sentieon/gvcftyper`, multi-`--resource:` parsing in `sentieon/varcal`, and the new `topic: versions` emission across all sentieon modules. Removed the now-broken explicit `versions.mix(SENTIEON_*.out.versions)` calls; sarek's `softwareVersionsToYAML` picks up the topic emissions via `channel.topic("versions")`.
- [#2194](https://github.com/nf-core/sarek/pull/2194) - Update `ensemblvep/vep` module: add `htslib` dependency, support apptainer container engine, fix cache input signature, fix output path patterns
- [#2194](https://github.com/nf-core/sarek/pull/2194) - Update `main.nf` to use lowercase `channel.*` factory methods (strict syntax)
- [#2203](https://github.com/nf-core/sarek/pull/2203) - Dedicated GHA for `Sentieon`

#### Fixed

- [#2117](https://github.com/nf-core/sarek/pull/2117) - Update alignment related files to strict syntax
- [#2129](https://github.com/nf-core/sarek/pull/2129) - Fix MuSE timestamp, swap to topics and change to strict syntax
- [#2165](https://github.com/nf-core/sarek/pull/2165) - Recover help message
- [#2167](https://github.com/nf-core/sarek/pull/2167) - Fix and extend pipeline level stub tests
- [#2170](https://github.com/nf-core/sarek/pull/2170) - Add index to workflow output for MultiQC
- [#2189](https://github.com/nf-core/sarek/pull/2189) - Preserve `groupKey` size hint into `groupTuple` in the sentieon haplotyper and dnascope subworkflows so per-sample MERGE*SENTIEON*\*\_VCFS / GVCFS emits progressively as each sample's intervals finish instead of bursting at end-of-haplotyper.
- [#2197](https://github.com/nf-core/sarek/pull/2197) - Fix controlfreec `versions` emission: swap to topics and remove explicit `versions.mix` wiring
- [#2217](https://github.com/nf-core/sarek/pull/2217) - Mark sentieon_dedup scenario in `save_output_as_bam` test with `sentieon: true` flag

#### Removed

## [3.8.1](https://github.com/nf-core/sarek/releases/tag/3.8.1) - Laitaure

Laitaure is a lake formed by the Rapaätno River in Sarek.

### Added

### Changed

### Fixed

- [#2128](https://github.com/nf-core/sarek/pull/2128) - Fix `bcftools concat` failing on Strelka somatic VCFs with non-contiguous chromosome blocks by adding `--allow-overlaps`

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |

### Parameters

| Params | status |
| ------ | ------ |

### Developer section

#### Added

#### Changed

- [#2134](https://github.com/nf-core/sarek/pull/2134) - Back to dev (3.9.0dev)

#### Fixed

#### Removed

## [3.8.0](https://github.com/nf-core/sarek/releases/tag/3.8.0) - Sitojaure

A mountain cabin near the Sami settlement between Saltoluokta and Kvikkjokk.

### Added

- [#2092](https://github.com/nf-core/sarek/pull/2092) - Add support for VEP Condel plugin to calculate Consensus Deleteriousness scores for missense mutations
- [#2093](https://github.com/nf-core/sarek/pull/2093) - Add support for VEP Mastermind plugin to retrieve citation counts from Mastermind Genomic Search Engine
- [#2094](https://github.com/nf-core/sarek/pull/2094) - Add support for VEP Phenotypes plugin to retrieve overlapping phenotype information from Ensembl databases
- [#2103](https://github.com/nf-core/sarek/pull/2103) - Documentation update about new VEP plugins
- [#2111](https://github.com/nf-core/sarek/pull/2111) - Add SnpSift annotation support using `--tools snpsift` with `--snpsift_databases` CSV configuration

### Changed

- [#2119](https://github.com/nf-core/sarek/pull/2119) - Update VEP version from 111.0-0 to 115.0-0 and VEP cache version from 114 to 115; update ensemblvep module to include `perl-math-cdf` dependency for Condel plugin

### Fixed

- [#2077](https://github.com/nf-core/sarek/pull/2077) - Remove re-indexed bam from `indexcov` from publishing into top level `outdir` directory
- [#2083](https://github.com/nf-core/sarek/pull/2083) - Remove `exists` validation from `snpeff_cache` and `vep_cache` parameters to fix workflow launch failures when annotation tools are not used
- [#2095](https://github.com/nf-core/sarek/pull/2095) - Fix typo in consensus calling parameter reference (used non-existent `params.consensus_vcfs` instead of `params.snv_consensus_calling`)
- [#2096](https://github.com/nf-core/sarek/pull/2096) - Fix consensus calling to include missing variant callers (`bcftools`, `lofreq`) and correct Sentieon tool names ([#2088](https://github.com/nf-core/sarek/issues/2088))
- [#2099](https://github.com/nf-core/sarek/pull/2099) - Remove deprecated `msisensor2_scan` parameter from schema and igenomes config to fix `nf-core pipelines schema build` validation error
- [#2100](https://github.com/nf-core/sarek/pull/2100) - Add missing citations for Condel, Mastermind, goleft indexcov, NGSCheckMate, SPRING, and vcflib to CITATIONS.md
- [#2109](https://github.com/nf-core/sarek/pull/2109) - Fix consensus calling to capture all variants from all callers by using `sites.txt` output; adds `CALLERS` and `NCALLERS` INFO fields to consensus VCF
- [#2113](https://github.com/nf-core/sarek/pull/2113) - Fix regex patterns for `dbnsfp_tbi`, `spliceai_snv`, and `spliceai_snv_tbi` parameter validation

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |

### Parameters

| Params                       | status  |
| ---------------------------- | ------- |
| `--vep_condel`               | added   |
| `--condel_config`            | added   |
| `--vep_mastermind`           | added   |
| `--mastermind_file`          | added   |
| `--mastermind_mutations`     | added   |
| `--mastermind_var_iden`      | added   |
| `--mastermind_url`           | added   |
| `--vep_phenotypes`           | added   |
| `--phenotypes_file`          | added   |
| `--phenotypes_file_tbi`      | added   |
| `--phenotypes_include_types` | added   |
| `--tools snpsift`            | added   |
| `--snpsift_databases`        | added   |
| `--msisensor2_scan`          | removed |

### Developer section

#### Added

#### Changed

- [#2076](https://github.com/nf-core/sarek/pull/2076) - Back to Dev
- [#2098](https://github.com/nf-core/sarek/pull/2098) - Starting workflow output migration with multiqc
- [#2101](https://github.com/nf-core/sarek/pull/2101) - Prepare release 3.8.0
- [#2126](https://github.com/nf-core/sarek/pull/2126) - Start versions migration to topics

#### Fixed

- [#2099](https://github.com/nf-core/sarek/pull/2099) - Fix `bbsplit.nf.test` input cardinality to match current PREPARE_GENOME subworkflow signature (31 parameters)
- [#2112](https://github.com/nf-core/sarek/pull/2112) - Fix BBSplit index building failure by adding null check for reads in `ext.prefix` configuration
- [#2120](https://github.com/nf-core/sarek/pull/2120) - Fix BBSplit index publish pattern from `bbmap` to `bbmap_index` to correctly save reference
- [#2104](https://github.com/nf-core/sarek/pull/2104) - Ignore warnings coming from singularity and conda
- [#2105](https://github.com/nf-core/sarek/pull/2105) - Ignore warnings coming from singularity
- [#2106](https://github.com/nf-core/sarek/pull/2106) - Fix conda setup in GHA

#### Removed

- [#2084](https://github.com/nf-core/sarek/pull/2084) - Removed no longer used old test profiles

## [3.7.1](https://github.com/nf-core/sarek/releases/tag/3.7.1) - Buollámtjåhkka

Buollámtjåhkka is the closest mountain to Saltoluokta and an easy peak to climb.

### Added

### Changed

- [#2073](https://github.com/nf-core/sarek/pull/2073) - Update MultiQC to version 1.33

### Fixed

- [#2069](https://github.com/nf-core/sarek/pull/2069) - Propagate tbi indices for HaplotypeCaller and Haplotyper to fix bug with merging vcfs and tbis.
- [#2071](https://github.com/nf-core/sarek/pull/2071) - Updated parameter validation to support the use of umi_read_structure along with umi_in_read_headers
- [#2073](https://github.com/nf-core/sarek/pull/2073) - Apply fix for BBSplit error: `unterminated s' command`
- [#2124](https://github.com/nf-core/sarek/pull/2124) - Fix FilterMutectCalls not running when starting from BAM with lane field in samplesheet

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| multiqc    | 1.31        | 1.33        |

### Parameters

| Params | status |
| ------ | ------ |

### Developer section

#### Added

- [#2144](https://github.com/nf-core/sarek/pull/2144) - Add developer guidelines document for human and AI contributors

#### Changed

- [#2067](https://github.com/nf-core/sarek/pull/2067) - Back to Dev

#### Fixed

#### Removed

## [3.7.0](https://github.com/nf-core/sarek/releases/tag/3.7.0) - Saltoluokta

Saltoluokta is a mountain lodge located in northern Sweden and a popular starting point into the Sarek Nationalpark.

This release includes a bump to Nextflow 25.10.2.

### Added

- [#2044](https://github.com/nf-core/sarek/pull/2044) - Add filtering with `bcftools view -f PASS,.` following variantcalling step
- [#2049](https://github.com/nf-core/sarek/pull/2049) - Add consensus calling of small variant VCFs for variants called by x or more tools, with `x=2` as default

### Changed

- [#2045](https://github.com/nf-core/sarek/pull/2045) - Propagate fastp shard naming if exists through BBSplit to ensure unique naming in Markduplicates
- [#2065](https://github.com/nf-core/sarek/pull/2065) - Bump minimal Nextflow version to 25.10.2

### Fixed

- [#2045](https://github.com/nf-core/sarek/pull/2045) - Propagate fastp shard naming if exists through BBSplit to ensure unique naming in Markduplicates
- [#2060](https://github.com/nf-core/sarek/pull/2060) - Update bbmap/bbsplit module to fix bbsplit index staging by using symlinks instead of full copy

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| nf-schema  | 2.4.2       | 2.6.1       |

### Parameters

| Params                       | status |
| ---------------------------- | ------ |
| `--filter_vcfs`              | New    |
| `--bcftools_filter_criteria` | New    |
| `--snv_consensus_calling`    | New    |
| `--consensus_min_count`      | New    |

### Developer section

#### Added

#### Changed

- [#1979](https://github.com/nf-core/sarek/pull/1979) - Update prepare_genome subworkflow to adhere to language server
- [#2041](https://github.com/nf-core/sarek/pull/2041) - Back to dev
- [#2043](https://github.com/nf-core/sarek/pull/2043) - Refactor postvariantcalling and split out varlociraptor from other options
- [#2048](https://github.com/nf-core/sarek/pull/2048) - No null value for snpeff_cache and vep_cache in tests
- [#2058](https://github.com/nf-core/sarek/pull/2058) - Template update for nf-core/tools v3.5.1
- [#2080](https://github.com/nf-core/sarek/pull/2080) - Improve test suite and capture stdout/err logs more efficiently

#### Fixed

- [#2053](https://github.com/nf-core/sarek/pull/2053) - Change yte input to one channel to disambiguate scenario file rendering
- [#2054](https://github.com/nf-core/sarek/pull/2054) - Fix typo on tbi_sentieon_dnascope channel
- [#2065](https://github.com/nf-core/sarek/pull/2065) - Bump nf-schema to 2.6.1, due to [nf-schema#181](https://github.com/nextflow-io/nf-schema/issues/181)

#### Removed

## [3.6.1](https://github.com/nf-core/sarek/releases/tag/3.6.1) - Sjnjierák

Sjnjierák is a popular stopover cabin on the way into the park.

This patch release includes a bump to Nextflow 25.04.8.

### Added

### Changed

### Fixed

- [2029](https://github.com/nf-core/sarek/pull/2029) - Correct intervals channel for parabricks

### Removed

### Dependencies

| Dependency   | Old version | New version |
| ------------ | ----------- | ----------- |
| `parabricks` | 4.5.1-1     | 4.6.0-1     |

### Parameters

| Params | status |
| ------ | ------ |

### Developer section

#### Added

#### Changed

- [2026](https://github.com/nf-core/sarek/pull/2026) - Back to dev
- [2038](https://github.com/nf-core/sarek/pull/2038) - Improve customising parabricks parameters docs

#### Fixed

#### Removed

## [3.6.0](https://github.com/nf-core/sarek/releases/tag/3.6.0) - Kvikkjokk

Kvikkjokk is a village where many trails start that lead through sarek.

### Added

- [1682](https://github.com/nf-core/sarek/pull/1682), [1770](https://github.com/nf-core/sarek/pull/1770) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files
- [1744](https://github.com/nf-core/sarek/pull/1744) - Add MuSE as new somatic variant caller
- [1804](https://github.com/nf-core/sarek/pull/1840) - Add parabricks/fq2bam as alternative to fastq_preprocess_gatk
- [1817](https://github.com/nf-core/sarek/pull/1817) - Added new contributor
- [1841](https://github.com/nf-core/sarek/pull/1841) - Add pcr-indel-model parameter for GATK HaplotypeCaller
- [1848](https://github.com/nf-core/sarek/pull/1848) - Add parameter for setting pixel distance for GATK MarkDuplicates
- [1856](https://github.com/nf-core/sarek/pull/1856) - Added early failure when more than 1 normal sample per patient is provided for somatic variant calling
- [1904](https://github.com/nf-core/sarek/pull/1904) - Icon support
- [1934](https://github.com/nf-core/sarek/pull/1934) - Add sentieon TNscope for tumour/normal variant calling
- [1937](https://github.com/nf-core/sarek/pull/1937) - Add UMI extraction for deduplication using fastp via `--umi_location`, `--umi_length` and `--umi_base_skip`
- [1937](https://github.com/nf-core/sarek/pull/1937) - Add consensus read generation when using sentieon dedup via `--sentieon_consensus`
- [1937](https://github.com/nf-core/sarek/pull/1937) - Add support for UMIs in read headers via `--umi_in_read_header`
- [1937](https://github.com/nf-core/sarek/pull/1937) - Use fgbio plugin to check read structure parameter is valid
- [1938](https://github.com/nf-core/sarek/pull/1938) - Add checks for uniqueness of sample ids and lane ids
- [1939](https://github.com/nf-core/sarek/pull/1939) - Modify config to add readgroups to fq2bam
- [1940](https://github.com/nf-core/sarek/pull/1940) - Add varlociraptor for variant calling
- [1953](https://github.com/nf-core/sarek/pull/1953) - Update freebayes and add QUAL filtering
- [1965](https://github.com/nf-core/sarek/pull/1965),[2017](https://github.com/nf-core/sarek/pull/2017) - Add msisensor2
- [1973](https://github.com/nf-core/sarek/pull/1973) - Update bcftools/annotate to pick up columns file input
- [2021](https://github.com/nf-core/sarek/pull/2021),[1983](https://github.com/nf-core/sarek/pull/1983) - Add BBsplit

### Changed

- [1682](https://github.com/nf-core/sarek/pull/1682) - Edit vcf_concatenate_germline subworkflow
- [1810](https://github.com/nf-core/sarek/pull/1810) - Move non-informative information in the CHANGELOG for the end user to its own Developer section
- [1890](https://github.com/nf-core/sarek/pull/1890) - Improve and update metro map
- [1903](https://github.com/nf-core/sarek/pull/1903) - Double the default `time` for all processes
- [1922](https://github.com/nf-core/sarek/pull/1922) - Update ASCAT module to v3.2.0
- [1937](https://github.com/nf-core/sarek/pull/1937) - Swapped from samblaster to samtools within the fgbio consensus generation
- [1961](https://github.com/nf-core/sarek/pull/1961) - Update ensemblvep cache version to 114
- [1961](https://github.com/nf-core/sarek/pull/1961) - Update ensemblvep cache version to 115
- [1961](https://github.com/nf-core/sarek/pull/1961) - Update ensemblvep modules to 114.2
- [1964](https://github.com/nf-core/sarek/pull/1964) - Update ensemblvep modules to 115.0
- [1982](https://github.com/nf-core/sarek/pull/1982) - Update ensemblvep modules to 115.1
- [1988](https://github.com/nf-core/sarek/pull/1988) - Update manta modules to latest build
- [1993](https://github.com/nf-core/sarek/pull/1993) - Update snpeff modules to 5.3.0a and ensemblvep modules to 115.2
- [2003](https://github.com/nf-core/sarek/pull/2003),[2005](https://github.com/nf-core/sarek/pull/2005) - Update subway map to clarify post-variantcalling processing options, and add BBSplit
- [2009](https://github.com/nf-core/sarek/pull/2009) - Update multiqc module to 1.31
- [2011](https://github.com/nf-core/sarek/pull/2011) - Downgrade snpeff db to at least 99 due to 105 not being available at the moment

### Fixed

- [1842](https://github.com/nf-core/sarek/pull/1842) - Updated the input validation of the pipeline to be more strict, thus preventing more issues when running the pipeline
- [1849](https://github.com/nf-core/sarek/pull/1849) - Fix bug in sample_lane_id definition in addReadgroupToMeta function
- [1858](https://github.com/nf-core/sarek/pull/1858) - Fix bug in parameter validation
- [1896](https://github.com/nf-core/sarek/pull/1896) - Add information on gatk_spark and save_output_as_bam
- [1928](https://github.com/nf-core/sarek/pull/1928) - Fix cnvkit when using --no_intervals, and correct cpu allocation
- [1937](https://github.com/nf-core/sarek/pull/1937) - Individual lanes are now merged together before fgbio consensus generation is performed
- [1992](https://github.com/nf-core/sarek/pull/1992) - Add `--sample_name` argument to deepvariant when `meta.sample` is available

### Removed

- [1806](https://github.com/nf-core/sarek/pull/1806) - Remove some files publication with the --concatenate_vcfs options

### Dependencies

| Dependency                             | Old version | New version |
| -------------------------------------- | ----------- | ----------- |
| `ascat`                                | 3.1.1       | 3.2.0       |
| `bcftools`                             | 1.20        | 1.21        |
| `deepvariant`                          | 1.8.0       | 1.9.0       |
| `ensemblvep`                           | 113.0       | 115.2       |
| `gawk`                                 | 5.1.0       | 5.3.0       |
| `fastp`                                | 0.23.4      | 0.24.0      |
| `fgbio`                                | 2.2.1       | 2.4.0       |
| `freebayes`                            | 1.3.6       | 1.3.10      |
| `gatk4`                                | 4.5.0.0     | 4.6.1.0     |
| `mosdepth`                             | 0.3.8       | 0.3.10      |
| `msisensor2`                           |             | 0.1         |
| `msisensorpro`                         | 1.2.0       | 1.3.0       |
| `multiqc`                              | 1.25.1      | 1.31        |
| `muse`                                 |             | 2.1.2       |
| `parabricks`                           |             | 4.5.1-1     |
| `rbt`                                  |             | 0.42.2      |
| `samblaster`                           | 0.1.26      | removed     |
| `samtools` (in `BWAMEM1_MEM`)          | 1.2         | 1.21        |
| `samtools` (in `BWAMEM2_MEM`)          | 1.19.2      | 1.21        |
| `samtools` (in `GATK4_MARKDUPLICATES`) | 1.19.2      | 1.21        |
| `sentieon`                             | 202308.03   | 202503.01   |
| `snpeff`                               | 5.1         | 5.3a        |
| `tabix`                                | 1.2         | 1.21        |
| `varlociraptor`                        |             | 8.7.4       |
| `vcflib`                               |             | 1.0.14      |
| `yte`                                  |             | 1.9.0       |

### Parameters

| Params                                | status |
| ------------------------------------- | ------ |
| `--freebayes_filter`                  | New    |
| `--msisensor2_models`                 | New    |
| `--msisensorpro_scan`                 | New    |
| `--sentieon_consensus`                | New    |
| `--umi_base_skip`                     | New    |
| `--umi_in_read_header`                | New    |
| `--umi_length`                        | New    |
| `--umi_location`                      | New    |
| `--umi_tag`                           | New    |
| `--varlociraptor_chunk_size`          | New    |
| `--varlociraptor_scenario_germline`   | New    |
| `--varlociraptor_scenario_somatic`    | New    |
| `--varlociraptor_scenario_tumor_only` | New    |

### Developer section

#### Added

- [1803](https://github.com/nf-core/sarek/pull/1803) - Back to dev
- [1806](https://github.com/nf-core/sarek/pull/1806) - Use `nft-vcf` for nf-test vcf assertions
- [1814](https://github.com/nf-core/sarek/pull/1814) - Added link to Bluesky
- [1815](https://github.com/nf-core/sarek/pull/1815) - Create nf-test pipeline vcf concatenation + normalize tests
- [1829](https://github.com/nf-core/sarek/pull/1829) - Add muse as variant caller to images
- [1835](https://github.com/nf-core/sarek/pull/1835) - Add GPU testing possibilities
- [1855](https://github.com/nf-core/sarek/pull/1855) - Add contributors info to the contributors field in the manifest
- [1922](https://github.com/nf-core/sarek/pull/1922) - Added tests for ASCAT

#### Changed

- [1761](https://github.com/nf-core/sarek/pull/1761) - Skip nf-test on docs changes
- [1806](https://github.com/nf-core/sarek/pull/1806) - Migrate pipeline pytest vcf concatenation tests to nf-test
- [1809](https://github.com/nf-core/sarek/pull/1809) - Replace `getReadsMD5()` by `readsMD5` from `nft-bam` plugin for more global cohesion with usage of `nft-vcf` plugin
- [1810](https://github.com/nf-core/sarek/pull/1810) - Implement automatic sharding for nf-test tests
- [1810](https://github.com/nf-core/sarek/pull/1810) - Skip all CI but linting on docs changes
- [1812](https://github.com/nf-core/sarek/pull/1812) - Move gatk based preprocessing to local subworkflow
- [1815](https://github.com/nf-core/sarek/pull/1815) - Migrate pipeline pytest vcf normalize tests to nf-test
- [1819](https://github.com/nf-core/sarek/pull/1819) - Migrate pipeline pytest tiddit tests to nf-test
- [1820](https://github.com/nf-core/sarek/pull/1820) - Migrate pipeline pytest manta tests to nf-test
- [1821](https://github.com/nf-core/sarek/pull/1821) - Migrate pipeline pytest freebayes tests to nf-test
- [1825](https://github.com/nf-core/sarek/pull/1825) - Migrate pipeline pytest cnvkit tests to nf-test
- [1826](https://github.com/nf-core/sarek/pull/1826) - Migrate pipeline pytest mpileup tests to nf-test
- [1827](https://github.com/nf-core/sarek/pull/1827) - Migrate pipeline pytest haplotypecaller tests to nf-test
- [1828](https://github.com/nf-core/sarek/pull/1828) - Migrate pipeline pytest lofreq tests to nf-test
- [1831](https://github.com/nf-core/sarek/pull/1831) - Migrate pipeline pytest fastp tests to nf-test
- [1832](https://github.com/nf-core/sarek/pull/1832) - Update all annotation related modules and subworkflows
- [1847](https://github.com/nf-core/sarek/pull/1847) - Runs on custom runners :rocket: thanks to [RunsOn](https://runs-on.com/)
- [1852](https://github.com/nf-core/sarek/pull/1852) - Ignore tests from modules
- [1852](https://github.com/nf-core/sarek/pull/1852) - Improve some nf-test tests
- [1866](https://github.com/nf-core/sarek/pull/1866) - Migrate pipeline pytest deepvariant tests to nf-test
- [1867](https://github.com/nf-core/sarek/pull/1867) - Migrate pipeline pytest gatk4spark tests to nf-test
- [1868](https://github.com/nf-core/sarek/pull/1868) - Migrate pipeline pytest intervals tests to nf-test
- [1871](https://github.com/nf-core/sarek/pull/1871) - Update all modules
- [1874](https://github.com/nf-core/sarek/pull/1874) - Migrate pipeline pytest joint_calling haplotypecaller tests to nf-test
- [1874](https://github.com/nf-core/sarek/pull/1874) - Migrate pipeline pytest joint_calling mutect2 tests to nf-test
- [1874](https://github.com/nf-core/sarek/pull/1874) - Migrate pipeline pytest mutect2 tests to nf-test
- [1874](https://github.com/nf-core/sarek/pull/1874) - More global cohesion in the all nf-test tests
- [1876](https://github.com/nf-core/sarek/pull/1876) - Migrate pipeline pytest ngscheckmate tests to nf-test
- [1877](https://github.com/nf-core/sarek/pull/1877) - Migrate pipeline pytest msisensorpro tests to nf-test
- [1878](https://github.com/nf-core/sarek/pull/1878) - Migrate pipeline pytest umi tests to nf-test
- [1879](https://github.com/nf-core/sarek/pull/1879) - Template update for nf-core/tools v3.2.1
- [1892](https://github.com/nf-core/sarek/pull/1892) - Make jobs automatically resubmit for exit code 175
- [1917](https://github.com/nf-core/sarek/pull/1917) - stub tests have stub tag
- [1927](https://github.com/nf-core/sarek/pull/1927) - Migrate pipeline pytest sentieon tests to nf-test
- [1932](https://github.com/nf-core/sarek/pull/1932) - Refactor and simplify pipeline test suite
- [1936](https://github.com/nf-core/sarek/pull/1936) - Template update for nf-core/tools v3.3.2
- [1953](https://github.com/nf-core/sarek/pull/1953) - Change freebayes tests from gzip to md5sum
- [1954](https://github.com/nf-core/sarek/pull/1954) - Refactor bcftools annotation subworkflows so that no diff is necessary from nf-core/modules
- [1962](https://github.com/nf-core/sarek/pull/1962) - Update gatk and gatk4spark applybqsr modules and subsequent subworkflows to deal with the newly added ext.suffix
- [1965](https://github.com/nf-core/sarek/pull/1965) - Refactor cram to bam conversion which is now is done even more upstream (following [1967](https://github.com/nf-core/sarek/pull/1967))
- [1967](https://github.com/nf-core/sarek/pull/1967) - Refactor muse subworkflows so that cram to bam conversion is done upstream
- [1967](https://github.com/nf-core/sarek/pull/1967) - Update msisensorpro modules to adhere to language server
- [1970](https://github.com/nf-core/sarek/pull/1970) - Update controlfreec modules to adhere to language server
- [1975](https://github.com/nf-core/sarek/pull/1975) - Now fails when no dbnsfp_tbi is provided when dbnsfp is
- [1977](https://github.com/nf-core/sarek/pull/1977) - Update sentieon modules to adhere to language server
- [1985](https://github.com/nf-core/sarek/pull/1985) - Update subway maps and workflow pictures to include msisensor2 following [1965](https://github.com/nf-core/sarek/pull/1965)
- [1990](https://github.com/nf-core/sarek/pull/1990) - Update parabricks/fq2bam to 4.5.1-1
- [2001](https://github.com/nf-core/sarek/pull/2001) - Remove lofreq VCF MD5sum - use summary
- [2007](https://github.com/nf-core/sarek/pull/2007) - Sort tools in test_full configs and add msisensor2
- [2008](https://github.com/nf-core/sarek/pull/2008), [2010](https://github.com/nf-core/sarek/pull/2010) - Skip conda tests that cannot be run due to lacking dependencies
- [2014](https://github.com/nf-core/sarek/pull/2014) - Prepare release and address comments

#### Fixed

- [1806](https://github.com/nf-core/sarek/pull/1806) - Fix some nf-test assertions
- [1809](https://github.com/nf-core/sarek/pull/1809) - Deals with nf-test snapshoting empty lists in a better way (https://github.com/nf-core/sarek/issues/1807)
- [1814](https://github.com/nf-core/sarek/pull/1814) - Fix link to GHA CI broken by [1810](https://github.com/nf-core/sarek/pull/1810)
- [1845](https://github.com/nf-core/sarek/pull/1845) - Modifying `.nftignore` should retrigger nf-test (cf https://github.com/nf-core/tools/pull/3508)
- [1852](https://github.com/nf-core/sarek/pull/1852) - Fix path to `license_message.py` script
- [1852](https://github.com/nf-core/sarek/pull/1852) - Modifying `assets/schema_input.json` and `nextflow_schema.json` should retrigger nf-test (cf https://github.com/nf-core/sarek/pull/1842)
- [1855](https://github.com/nf-core/sarek/pull/1855) - Fix json schema cf_chrom_len input broken by [1842](https://github.com/nf-core/sarek/pull/1842)
- [1859](https://github.com/nf-core/sarek/pull/1859) - Fix: change dbsnp channel from queue to value in muse subworkflow, wrong implemented in [1744](https://github.com/nf-core/sarek/pull/1744)
- [1899](https://github.com/nf-core/sarek/pull/1899) - Ensure nf-test runs for all profiles on release
- [1917](https://github.com/nf-core/sarek/pull/1917) - Ensure all versions and reports are reported to MultiQC
- [1927](https://github.com/nf-core/sarek/pull/1927) - Fixed Sentieon variant calling broken by [1871](https://github.com/nf-core/sarek/pull/1871)
- [1930](https://github.com/nf-core/sarek/pull/1930) - Fixed tests when no sentieon license/ENV are provided
- [1932](https://github.com/nf-core/sarek/pull/1932) - Fix typo for in UMI warning message
- [1933](https://github.com/nf-core/sarek/pull/1933) - Correct link in README
- [1935](https://github.com/nf-core/sarek/pull/1935) - Fix bug in samplesheet_to_channel workflow due to bad integer handling with lane
- [1984](https://github.com/nf-core/sarek/pull/1984) - Fix tuple mismatch in GATK_BASERECALIBRATOR
- [1996](https://github.com/nf-core/sarek/pull/1996) - MuSE: change to htslib for bgzip and tabix & language server
- [1998](https://github.com/nf-core/sarek/pull/1998) - Adjust VEP versions in snap files with corrected module
- [2002](https://github.com/nf-core/sarek/pull/2002) - Update strelka to specific build to fix error in somatic mode
- [2013](https://github.com/nf-core/sarek/pull/2013) - Fix snaps after MultiQC update
- [2019](https://github.com/nf-core/sarek/pull/2019) - Allow other cloud buckets than `s3://annotation-cache/` for the VEP and snpEff cache

#### Removed

- [1814](https://github.com/nf-core/sarek/pull/1814) - Removed link to Twitter/X
- [1884](https://github.com/nf-core/sarek/pull/1884) - Remove pytest-workflow from CI (copied from [1729](https://github.com/nf-core/sarek/pull/1729))
- [1956](https://github.com/nf-core/sarek/pull/1956) - Remove tests for downloading cache (Snpeff and VEP) (we already have tests for the cache in the modules)
- [1957](https://github.com/nf-core/sarek/pull/1957) - Remove duplicated gpu profile from config
- [1994](https://github.com/nf-core/sarek/pull/1994) - Prevent conda profile running on gpu
- [1995](https://github.com/nf-core/sarek/pull/1995) - Remove md5sums of png files for controlfreec
- [1997](https://github.com/nf-core/sarek/pull/1997) - Remove png and pdf md5sums for all variant callers
- [2004](https://github.com/nf-core/sarek/pull/2004) - Remove .cram.metrics and .cram.metrics.multiqc.tsv md5sums for sentieon

## [3.5.1](https://github.com/nf-core/sarek/releases/tag/3.5.1) - Akkatjåkkå

Akkatjåkkå is another glacier.

### Added

- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev

### Changed

- [1767](https://github.com/nf-core/sarek/pull/1767) - Bump nf-schema version to 2.2.1
- [1777](https://github.com/nf-core/sarek/pull/1777) - Merge intervals for WES in GATK GenomicsDBImport
- [1798](https://github.com/nf-core/sarek/pull/1798) - Prepare release 3.5.1

### Fixed

- [1797](https://github.com/nf-core/sarek/pull/1797) - Use `file-path-pattern` over `file-path` to hanlde glob for `known_indels` and `known_indels_tbi` to fix [1785](https://github.com/nf-core/sarek/issues/1785)
- [1802](https://github.com/nf-core/sarek/pull/1802) - Update GHA for full_test tests

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |

### Parameters

| Params | Status |
| ------ | ------ |

## [3.5.0](https://github.com/nf-core/sarek/releases/tag/3.5.0) - Áhkájiegna

A set of connecting glaciers.

### Added

- [1613](https://github.com/nf-core/sarek/pull/1613) - add indexcov
- [1638](https://github.com/nf-core/sarek/pull/1638) - Added additional documentation detailing ASCAT WES usage.
- [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller
- [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev
- [1653](https://github.com/nf-core/sarek/pull/1653) - Updates `sarek_subway` files with `lofreq`
- [1660](https://github.com/nf-core/sarek/pull/1642) - Add `--length_required` for minimal reads length with `FASTP`
- [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update
- [1664](https://github.com/nf-core/sarek/pull/1664) - Check if flowcell ID matches for read pair
- [1730](https://github.com/nf-core/sarek/pull/1730) - Enable Harshil Alignment™️ in VS Code workspace settings

### Changed

- [1579](https://github.com/nf-core/sarek/pull/1579) - Update Sentieon usage docs
- [1635](https://github.com/nf-core/sarek/pull/1635) - Fix docs to reflect variant calling tool - data type correctly
- [1668](https://github.com/nf-core/sarek/pull/1668) - Add nf-test sharding CI
- [1669](https://github.com/nf-core/sarek/pull/1669) - Better nf-test pipeline level tests
- [1677](https://github.com/nf-core/sarek/pull/1677) - Migrate pytest aligner and pipeline default tests to nf-test
- [1680](https://github.com/nf-core/sarek/pull/1680) - Template update for nf-core/tools v3.0.0
- [1681](https://github.com/nf-core/sarek/pull/1681) - Template update for nf-core/tools v3.0.1
- [1686](https://github.com/nf-core/sarek/pull/1686) - Template update for nf-core/tools v3.0.2
- [1692](https://github.com/nf-core/sarek/pull/1692) - Update ensemblvep
- [1695](https://github.com/nf-core/sarek/pull/1695) - Update all modules
- [1707](https://github.com/nf-core/sarek/pull/1707) - Un-hide parameters and clean up Json schema
- [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test
- [1711](https://github.com/nf-core/sarek/pull/1711) - Migrate pipeline pytest strelka tests to nf-test
- [1731](https://github.com/nf-core/sarek/pull/1731) - Migrate pipeline pytest controlfreec tests to nf-test

### Fixed

- [1624](https://github.com/nf-core/sarek/pull/1624) - Fix channel stalling for bcftools index
- [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
- [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests
- [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge
- [1693](https://github.com/nf-core/sarek/pull/1693) - Fixes flowcell retrieval during samplesheet parsing
- [1694](https://github.com/nf-core/sarek/pull/1694) - Fix manifest DOI display on CLI
- [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json
- [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode
- [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet
- [1743](https://github.com/nf-core/sarek/pull/1743) - Add setup java 17 in GHA for latest Nextflow version
- [1745](https://github.com/nf-core/sarek/pull/1745) - Fix bug where workflow can hang if the email parameter is set
- [1746](https://github.com/nf-core/sarek/pull/1746) - Fix Sentieon module inputs
- [1752](https://github.com/nf-core/sarek/pull/1752) - Add `indexcov` and `lofreq` to full size tests. Amend overview figures.
- [1754](https://github.com/nf-core/sarek/pull/1754) - Fix test string
- [1755](https://github.com/nf-core/sarek/pull/1755) - Remove `default` channel and name from local modules
- [1757](https://github.com/nf-core/sarek/pull/1757) - Fix Changelog by adding missing new parameters

### Removed

- [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
- [1709](https://github.com/nf-core/sarek/pull/1709) - Remove `Strelka` tumor-only somatic variant calling
- [1728](https://github.com/nf-core/sarek/pull/1728) - Remove BAM to CRAM conversion of input files for post-alignment entry points

### Dependencies

| Dependency    | Old version | New version |
| ------------- | ----------- | ----------- |
| `coreutils`   | 8.30        | 9.5         |
| `deepvariant` | 1.5.0       | 1.6.1       |
| `ensemblvep`  | 111.0       | 113.0       |
| `fgbio`       | 2.0.2       | 2.1.2       |
| `gawk`        | 5.1.0       | 5.3.0       |
| `htslib`      | 1.20        | 1.21        |
| `lofreq`      |             | 2.1.5       |
| `multiqc`     | 1.21        | 1.25.1      |
| `samtools`    | 1.20        | 1.21        |
| `sentieon`    | 202308.02   | 202308.03   |
| `svdb`        | 2.8.1       | 2.8.2       |

### Parameters

| Params                               | Status  |
| ------------------------------------ | ------- |
| `--help_full`                        | New     |
| `--length_required`                  | New     |
| `--show_hidden`                      | New     |
| `--snpeff_db`                        | Updated |
| `--snpeff_genome`                    | Removed |
| `--validationFailUnrecognisedParams` | Removed |
| `--validationLenientMode`            | Removed |
| `--validationSchemaIgnoreParams`     | Removed |
| `--validationShowHiddenParams`       | Removed |

## [3.4.4](https://github.com/nf-core/sarek/releases/tag/3.4.4) - Ruopsokjåkhå

Ruopsokjåkhå is another peak of the Pårte massif.

### Added

- [1614](https://github.com/nf-core/sarek/pull/1614) - Back to dev
- [1639](https://github.com/nf-core/sarek/pull/1639) - Bump version to prepare release

### Changed

- [1627](https://github.com/nf-core/sarek/pull/1627) - Correct tower reports/snpeff format

### Fixed

- [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation
- [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |

### Parameters

## [3.4.3](https://github.com/nf-core/sarek/releases/tag/3.4.3) - Loametjåhkkå

Loametjåhkkå is another one of the main peaks of the Pårte massif.

### Added

- [#1502](https://github.com/nf-core/sarek/pull/1502) - export CNVs into VCF format in `bam_variant_calling_cnvkit`
- [#1534](https://github.com/nf-core/sarek/pull/1534), [#1573](https://github.com/nf-core/sarek/pull/1573), [#1734](https://github.com/nf-core/sarek/pull/1534) - Handling `.fastq.gz.spring` files as input
- [#1593](https://github.com/nf-core/sarek/pull/1593) - Prepare release `3.4.2`

### Changed

- [#1502](https://github.com/nf-core/sarek/pull/1502) - Improved handling of CNVkit reference
- [#1502](https://github.com/nf-core/sarek/pull/1502) - Specific CNV call step, with recommended settings for germline
- [#1508](https://github.com/nf-core/sarek/pull/1508) - Sync `TEMPLATE` with `tools` `2.14.0`
- [#1513](https://github.com/nf-core/sarek/pull/1513) - Back to dev
- [#1518](https://github.com/nf-core/sarek/pull/1518) - Sync `TEMPLATE` with `tools` `2.14.1`
- [#1521](https://github.com/nf-core/sarek/pull/1521) - Minor code refactoring to simplify syntax in args handling
- [#1545](https://github.com/nf-core/sarek/pull/1545) - Update modules
- [#1552](https://github.com/nf-core/sarek/pull/1552) - Update samtools to v1.20
- [#1545](https://github.com/nf-core/sarek/pull/1545) - Update modules
- [#1553](https://github.com/nf-core/sarek/pull/1553) - Update bcftools to v1.20
- [#1557](https://github.com/nf-core/sarek/pull/1557) - Update ENSEMBLVEP cache to 111

### Fixed

- [#1536](https://github.com/nf-core/sarek/pull/1536) - Correct typo `Strelka2` to `Strelka`
- [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
- [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
- [#1547](https://github.com/nf-core/sarek/pull/1547) - Correct typo in help text in nextflow_schema.json
- [#1556](https://github.com/nf-core/sarek/pull/1556) - Fix display of some commands in `docs/usage.md`
- [#1563](https://github.com/nf-core/sarek/pull/1563) - Fix `vep_cache_path_full` so that `--refseq/--merged` will work for ENSEMBLVEP
- [#1570](https://github.com/nf-core/sarek/pull/1570) - Remove duplicated notes in FASTQC output docs
- [#1596](https://github.com/nf-core/sarek/pull/1596) - Fix haplotypecaller tests
- [#1597](https://github.com/nf-core/sarek/pull/1597) - Fix deepvariant tests
- [#1612](https://github.com/nf-core/sarek/pull/1612) - Remove empty output directories

### Removed

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `bcftools` | 1.18        | 1.20        |
| `bwa`      | 0.7.17      | 0.7.18      |
| `cnvkit`   | 0.9.10      | 0.9.11      |
| `htslib`   | 1.19.1      | 1.20        |
| `samtools` | 1.19.2      | 1.20        |

### Parameters

## [3.4.2](https://github.com/nf-core/sarek/releases/tag/3.4.2) - Sájtáristjåhkkå

Sájtáristjåhkkå is another peak (just under 2k) in the Pårte massif, it is one of the few peaks in Sweden that cannot be climbed without proper climbing equipment.

### Added

- [#1489](https://github.com/nf-core/sarek/pull/1489) - Added a `testdata.nf-core.sarek` key in `conf/igenomes.config` for small reference
- [#1493](https://github.com/nf-core/sarek/pull/1493) - Added a `wave` profile
- [#1498](https://github.com/nf-core/sarek/pull/1498) - Prepare release `3.4.2`

### Changed

- [#1477](https://github.com/nf-core/sarek/pull/1477) - Back to dev
- [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2`
- [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication
- [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02`
- [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8`
- [#1505](https://github.com/nf-core/sarek/pull/1505) - Update CITATIONS.md
- [#1506](https://github.com/nf-core/sarek/pull/1506) - Fixing typos (`index_alignement` -> `index_alignment`)
- [#1509](https://github.com/nf-core/sarek/pull/1509) - Update contributors

### Fixed

- [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix
- [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline`
- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491)
- [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest
- [#1499](https://github.com/nf-core/sarek/pull/1499) - Remove all md5sum for mosdepth tests
- [#1499](https://github.com/nf-core/sarek/pull/1499) - Add mosdepth dependency to all tests runnning it
- [#1501](https://github.com/nf-core/sarek/pull/1501) - Remove string "None" param option from ascat_genome

### Removed

- [#1489](https://github.com/nf-core/sarek/pull/1489) - Remove `test_cache` profile

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `mosdepth` | 0.3.6       | 0.3.8       |
| `sentieon` | 202308.01   | 202308.02   |

### Modules / Subworkflows

### Parameters

## [3.4.1](https://github.com/nf-core/sarek/releases/tag/3.4.1) - Balgattjåhkkå

Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the other one being Pårtetjåkko (Bårddetjåhkkå).

### Added

- [#1272](https://github.com/nf-core/sarek/pull/1372) - Add integration with NCBench: Automatic submission of latest benchmarking runs
- [#1333](https://github.com/nf-core/sarek/pull/1333) - Back to dev
- [#1335](https://github.com/nf-core/sarek/pull/1335) - Add index computation of `bcftools_annotations`, if not provided
- [#1340](https://github.com/nf-core/sarek/pull/1340) - Adds Azure test profiles and megatests
- [#1372](https://github.com/nf-core/sarek/pull/1372) - Add NCBench test profile for Agilent datasets
- [#1409](https://github.com/nf-core/sarek/pull/1409) - Add params `modules_testdata_base_path` to test profile

### Changed

- [#1339](https://githu.com/nf-core/sarek/pull/1339), [#1401](https://github.com/nf-core/sarek/pull/1401) - Update sentieon-modules to Sentieon `202308.01` and adding support for running Sentieon with Conda and Apptainer
- [#1344](https://github.com/nf-core/sarek/pull/1344) - Enable CRAM QC, when starting from variantcalling
- [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local modules
- [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local subworkflows
- [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11`
- [#1385](https://github.com/nf-core/sarek/pull/1385), [#1436](https://github.com/nf-core/sarek/pull/1436) - Sync `TEMPLATE` with `tools` `2.12`
- [#1408](https://github.com/nf-core/sarek/pull/1408), [#1412](https://github.com/nf-core/sarek/pull/1412) - Updating samtools to v1.19.2 - except in GATK/markduplicates. (Temporarily disabled nf-test for bwamem2/mem.)
- [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporarily disable sentieon related tests
- [#1414](https://github.com/nf-core/sarek/pull/1414) - Sync `TEMPLATE` with `tools` `2.13`
- [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates
- [#1426](https://github.com/nf-core/sarek/pull/1426) - Updating certain modules in order to fix the testdata-path in the nf-tests of those modules. Setting Docker runOptions for params.use_gatk_spark
- [#1428](https://github.com/nf-core/sarek/pull/1428) - Sync `TEMPLATE` with `tools` `2.13.1`
- [#1422](https://github.com/nf-core/sarek/pull/1422) - Refactoring following `TEMPLATE` sync with `tools` `2.13`
- [#1431](https://github.com/nf-core/sarek/pull/1431) - Using docker.containerOptions instead of docker.runOptions. Clearing containerOptions for SPARK modules for any kind of supported container engine
- [#1439](https://github.com/nf-core/sarek/pull/1439) - Replacing the local module `BUILD_INTERVALS` with the nf-core module `GAWK`
- [#1456](https://github.com/nf-core/sarek/pull/1456), [#1472](https://github.com/nf-core/sarek/pull/1472), [#1473](https://github.com/nf-core/sarek/pull/1473) - Revert usage of docker.runOptions. Add an empty docker.runOptions when using the new `spark` profile
- [#1457](https://github.com/nf-core/sarek/pull/1457) - Update all modules
- [#1466](https://github.com/nf-core/sarek/pull/1466) - Update `VEP`

### Fixed

- [#1334](https://github.com/nf-core/sarek/pull/1334) - Remove extra v, when reporting tower runs on slack
- [#1335](https://github.com/nf-core/sarek/pull/1335) - Add docs and validation for bcftools annotation parameters
- [#1345](https://github.com/nf-core/sarek/pull/1345) - Preserve STDERR for easier debugging
- [#1351](https://github.com/nf-core/sarek/pull/1351) - Fix params name for test profiles (`bcftools_annotations`)
- [#1357](https://github.com/nf-core/sarek/pull/1364) - Fixed bug where samples were dropped while reconstituting BAM files
- [#1373](https://github.com/nf-core/sarek/pull/1373) - Add `chr` prefix to NCBench bed file & enable trimming
- [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
- [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation
- [#1390](https://github.com/nf-core/sarek/pull/1390) - Fix badges in README
- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2
- [#1403](https://github.com/nf-core/sarek/pull/1403) - Fix intervals usage with dot in chromosome names
- [#1407](https://github.com/nf-core/sarek/pull/1407) - Fix CI tests name
- [#1420](https://github.com/nf-core/sarek/pull/1420) - Make `-a` a default argument for `bcftools` concat
- [#1422](https://github.com/nf-core/sarek/pull/1422) - Fix `Cannot serialize context map` warning
- [#1462](https://github.com/nf-core/sarek/pull/1462) - Fix ascat input channels
- [#1463](https://github.com/nf-core/sarek/pull/1463) - Add `spark` profile to all gatk4spark tests
- [#1465](https://github.com/nf-core/sarek/pull/1465), [#1469](https://github.com/nf-core/sarek/pull/1469) - Fix input channels and tests of Sentieon workflows
- [#1470](https://github.com/nf-core/sarek/pull/1470) - Fix channels for `MultiQC`
- [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `snpeff_db` params to `validationSchemaIgnoreParams` to fix issues with Seqera Platform
- [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `vep_cache_version` params to `validationSchemaIgnoreParams` to fix [#1454](https://github.com/nf-core/sarek/issues/1454)
- [#1471](https://github.com/nf-core/sarek/pull/1471) - Update `vep_version` params match the actual tool version
- [#1472](https://github.com/nf-core/sarek/pull/1472) - Cast `snpeff_db` params as a string to fix issues with Seqera Platform, as [#1471](https://github.com/nf-core/sarek/pull/1471) was not working as expected
- [#1472](https://github.com/nf-core/sarek/pull/1472) - Load `spark` profile last to avoid issues with `test` profiles

### Removed

- [#1405](https://github.com/nf-core/sarek/pull/1405) - Removing docker.userEmulation

### Dependencies

| Dependency   | Old version | New version |
| ------------ | ----------- | ----------- |
| `bcftools`   | 1.17        | 1.18        |
| `ensemblvep` | 110.0       | 111.0       |
| `fgbio`      | 2.0.2       | 2.1.0       |
| `gatk`       | 4.4.0.0     | 4.5.0.0     |
| `gatk-spark` | 4.4.0.0     | 4.5.0.0     |
| `mosdepth`   | 0.3.3       | 0.3.6       |
| `multiqc`    | 1.17        | 1.18        |
| `samtools`   | 1.17        | 1.19.2      |

### Modules / Subworkflows

| script | Old name | New name |
| ------ | -------- | -------- |

### Parameter

| Old name                     | New name                   |
| ---------------------------- | -------------------------- |
| `bcftools_annotations_index` | `bcftools_annotations_tbi` |

## [3.4.0](https://github.com/nf-core/sarek/releases/tag/3.4.0) - Pårtetjåkko

Pårtetjåkko is a mountain in the south of the park.

### Added

- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module
- [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline
- [#1244](https://github.com/nf-core/sarek/pull/1244) - Add bcf annotate module
- [#1252](https://github.com/nf-core/sarek/pull/1252) - Added NGSCheckMate tool for checking that samples come from the same individual
- [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev
- [#1288](https://github.com/nf-core/sarek/pull/1288) - Add nf-test continuous integration (but no tests)
- [#1290](https://github.com/nf-core/sarek/pull/1290) - Add nf-test for whole pipeline

### Changed

- [#1278](https://github.com/nf-core/sarek/pull/1278) - Hide sentieon parameters similar to other variant callers
- [#1280](https://github.com/nf-core/sarek/pull/1280) - Replacing link to `SentieonDNAscopeModel1.1.model` in Sentieon's S3 with link to same file in igenomes' S3
- [#1303](https://github.com/nf-core/sarek/pull/1303) - Ressurect vep_version params and changed its scope to pipeline to enable usage for vep loftee plugin
- [#1304](https://github.com/nf-core/sarek/pull/1304) - Update modules
- [#1311](https://github.com/nf-core/sarek/pull/1311) - Update local modules with an `environment.yml` file
- [#1317](https://github.com/nf-core/sarek/pull/1317) - Add new tools to subway map
- [#1325](https://github.com/nf-core/sarek/pull/1325) - Move `sentieon_dnascope_model` params into `igenomes.config`
- [#1325](https://github.com/nf-core/sarek/pull/1325) - Refactor config files
- [#1327](https://github.com/nf-core/sarek/pull/1327) - Update modules to have an conda environment name

### Fixed

- [#1277](https://github.com/nf-core/sarek/pull/1277) - Fix null value issue for Mutect2 joint calling
- [#1287](https://github.com/nf-core/sarek/pull/1287) - Adding label `process_single` to local modules
- [#1298](https://github.com/nf-core/sarek/pull/1298) - Fix annotation cache usage
- [#1301](https://github.com/nf-core/sarek/pull/1301) - Fix nf-prov usage
- [#1315](https://github.com/nf-core/sarek/pull/1315) - Avoid clash of configs of `FILTERVARIANTTRANCHES` in the Sentieon-Haplotyper and GATK-Haplotypecaller subworkflows
- [#1318](https://github.com/nf-core/sarek/pull/1218) - Fix writing of params.json on S3
- [#1324](https://github.com/nf-core/sarek/pull/1324) - Fix various typos & code formatting
- [#1325](https://github.com/nf-core/sarek/pull/1325) - Update bcfannotate tests and related config files
- [#1328](https://github.com/nf-core/sarek/pull/1328) - Fix links to docs in `nextflow_schema.json` and `docs/output.md`
- [#1328](https://github.com/nf-core/sarek/pull/1328) - Add missing icons in `nextflow_schema.json`
- [#1330](https://github.com/nf-core/sarek/pull/1330) - Add SnpEff to full sized tests

### Removed

- [#1298](https://github.com/nf-core/sarek/pull/1298) - Remove `--use_annotation_cache_keys` params

### Dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `fastqc`   | 0.11.9      | 0.12.1      |
| `multiqc`  | 1.15        | 1.17        |

### Modules / Subworkflows

| script                        | Old name                      | New name                      |
| ----------------------------- | ----------------------------- | ----------------------------- |
| `gatk4spark/applybqsr`        | `GATK4_APPLYBQSRSPARK`        | `GATK4SPARK_APPLYBQSR`        |
| `gatk4spark/baserecalibrator` | `GATK4_BASERECALIBRATORSPARK` | `GATK4SPARK_BASERECALIBRATOR` |
| `gatk4spark/markduplicates`   | `GATK4_MARKDUPLICATESSPARK`   | `GATK4SPARK_MARKDUPLICATES`   |

## [3.3.2](https://github.com/nf-core/sarek/releases/tag/3.3.2) - Ráhpajávvre

Ráhpajávvre is the Lule Sámi spelling of Rapaselet.

### Added

- [#1246](https://github.com/nf-core/sarek/pull/1246) - Back to dev
- [#1259](https://github.com/nf-core/sarek/pull/1259) - nf-prov plugin
- [#1288](https://github.com/nf-core/sarek/pull/1288) - Add nf-test continuous integration

### Changed

- [#1248](https://github.com/nf-core/sarek/pull/1248) - Improve annotation-cache docs
- [#1261](https://github.com/nf-core/sarek/pull/1261) - Enable cache for annotation generation when using 'merge'

### Fixed

- [#1247](https://github.com/nf-core/sarek/pull/1247) - FIX: Result paths for full size test to be correctly displayed on the website
- [#1256](https://github.com/nf-core/sarek/pull/1256) - Fix issue with controlfreec container declaration
- [#1270](https://github.com/nf-core/sarek/pull/1270) - Revert controlfreec/assesssignificance module to 11.6

### Dependencies

| Dependency                         | Old version | New version |
| ---------------------------------- | ----------- | ----------- |
| `Control-FREEC/assesssignificance` | 11.6b       | 11.6        |

## [3.3.1](https://github.com/nf-core/sarek/releases/tag/3.3.1) - Biellorippjávrre

A lake near the Rapaselet delta.

### Added

- [#1231](https://github.com/nf-core/sarek/pull/1231) - Back to dev

### Changed

- [#1242](https://github.com/nf-core/sarek/pull/1242) - Simplify sentieon nf-core test license usage
- [#1243](https://github.com/nf-core/sarek/pull/1243) - Improve json schema usage for input

### Fixed

- [#1232](https://github.com/nf-core/sarek/pull/1232) - Fix Zenodo IDs in manifest
- [#1236](https://github.com/nf-core/sarek/pull/1236) - Fix annotation cache folder verification when no annotation
- [#1240](https://github.com/nf-core/sarek/pull/1240) - Disable JVM Hotspot in all modules/gatk4 ([#1030](https://github.com/nf-core/sarek/issues/1030))
- [#1241](https://github.com/nf-core/sarek/pull/1241) - Fix axis text of controlfreec plots closing [#921](https://github.com/nf-core/sarek/issues/921)

### Dependencies

| Dependency      | Old version | New version |
| --------------- | ----------- | ----------- |
| `Control-FREEC` | 11.6        | 11.6b       |

## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet

Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe massif (formerly written Piellorieppe) and the Skårki massif.

### Added

- [#930](https://github.com/nf-core/sarek/pull/930) - Add more manual tests
- [#1130](https://github.com/nf-core/sarek/pull/1130) - Back to dev
- [#1013](https://github.com/nf-core/sarek/pull/1013) - Mutect2 multi sample mode with `--joint_mutect2`
- [#1153](https://github.com/nf-core/sarek/pull/1153) - Add input validation for Sentieon & FGBio UMI incompatibility
- [#1158](https://github.com/nf-core/sarek/pull/1158) - Add preprint
- [#1159](https://github.com/nf-core/sarek/pull/1159) - ISMB Poster
- [#1173](https://github.com/nf-core/sarek/pull/1173) - CI tests for VQSR track with stub runs
- [#1122](https://github.com/nf-core/sarek/pull/1122), [#1196](https://github.com/nf-core/sarek/pull/1196) - Add `annotation cache` functionality
- [#1184](https://github.com/nf-core/sarek/pull/1184) - Stub-based CI-test of Sentieon joint-germline variant-calling with VQSR

### Changed

- [#1151](https://github.com/nf-core/sarek/pull/1151) - Refactor codebase
- [#1157](https://github.com/nf-core/sarek/pull/1157) - Move all vep args from `ext.args` to `params.vep_custom_args` to allow easier modifications
- [#1059](https://github.com/nf-core/sarek/pull/1059) - Add `nf-validation` for samplesheet validation
- [#1160](https://github.com/nf-core/sarek/pull/1160) - Updating tiddit to v3.6.1
- [#1166](https://github.com/nf-core/sarek/pull/1166) - More info about `--tools`
- [#1173](https://github.com/nf-core/sarek/pull/1173) - Refactor single sample filtering of Haplotypecaller generated VCFs ([#1053](https://github.com/nf-core/sarek/pull/1053))
- [#1174](https://github.com/nf-core/sarek/pull/1174) - Updating multiqc to v1.15
- [#1179](https://github.com/nf-core/sarek/pull/1179) - Unhide params `trim_fastq`, `umi_read_structure`, and `aligner`
- [#1180](https://github.com/nf-core/sarek/pull/1180) - Updating the nf-core modules
- [#1198](https://github.com/nf-core/sarek/pull/1198) - Prepare release `3.3.0`
- [#1200](https://github.com/nf-core/sarek/pull/1200) - Streamline Github Actions workflows
- [#1212](https://github.com/nf-core/sarek/pull/1212) - Use matrix for AWS megatests
- [#1218](https://github.com/nf-core/sarek/pull/1218) - Remove Singularity tests for GHA
- [#1227](https://github.com/nf-core/sarek/pull/1227) - Update modules

### Fixed

- [#1143](https://github.com/nf-core/sarek/pull/1143) - `snpeff_db` is now a string
- [#1145](https://github.com/nf-core/sarek/pull/1145) - Fixed Zenodo links in `README.md` and in `WorkflowMain.groovy`
- [#1149](https://github.com/nf-core/sarek/pull/1149) - Update `Manta` modules and fix usage of `--exome` flag
- [#1155](https://github.com/nf-core/sarek/pull/1155) - Restore proper rendering in `usage.md`
- [#1163](https://github.com/nf-core/sarek/pull/1163) - Correcting location of output folder for joint variant calling with GATK's haplotypecaller
- [#1169](https://github.com/nf-core/sarek/pull/1169) - Updating Sentieon-modules. (The conda-check in the Sentieon-modules was moved to the script-section. The version of Sentieon remain unchanged.)
- [#1171](https://github.com/nf-core/sarek/pull/1171) - Fix channel logic for germline resource to skip GetPileupSummary if not provided
- [#1172](https://github.com/nf-core/sarek/pull/1172) - Publish gvcf files when all intervals are processed at once ([#764](https://github.com/nf-core/sarek/issues/764))
- [#1173](https://github.com/nf-core/sarek/pull/1173) - Fixed duplicated entries in joint germline recalibrated VCF ([#966](https://github.com/nf-core/sarek/pull/966), [#1102](https://github.com/nf-core/sarek/pull/1102)),
  fixed grouping joint germline recalibrated VCF ([#1137](https://github.com/nf-core/sarek/pull/1137))
- [#1177](https://github.com/nf-core/sarek/pull/1177) - Fix status inference when using nf-validation plugin
- [#1181](https://github.com/nf-core/sarek/pull/1181) - Fix join mismatch error in Mutect2 tumor only subworkflow
- [#1183](https://github.com/nf-core/sarek/pull/1183) - Add docs for concatentated germline variants
- [#1184](https://github.com/nf-core/sarek/pull/1184) - Fix issue with duplicated variants in VCF from Sentieon-based joint-germline variant-calling with VQSR. (Corresponding to [#966](https://github.com/nf-core/sarek/issues/966) for GATK.)
- [#1192](https://github.com/nf-core/sarek/pull/1192) - Add `ASCATprofile.png` to ASCAT output docs
- [#1197](https://github.com/nf-core/sarek/pull/1197) - Improve `tower.yml` file to display reports in Tower ([#1190](https://github.com/nf-core/sarek/issues/1190))
- [#1202](https://github.com/nf-core/sarek/pull/1202) - Remove GHA step that caches Nextflow and bump other out of date actions
- [#1203](https://github.com/nf-core/sarek/pull/1203) - Fix issue with Singularity containers on test profiles
- [#1204](https://github.com/nf-core/sarek/pull/1204) - Fix issue with nf-validation: lane can be a requirement of bam too now
- [#1205](https://github.com/nf-core/sarek/pull/1205) - Less tests triggered
- [#1214](https://github.com/nf-core/sarek/pull/1214) - Don't pass in intervals file to ControlFREEC for WGS analysis
- [#1215](https://github.com/nf-core/sarek/pull/1215) - Fix `meta.id` for mutect2 tumor_only subworkflows
- [#1216](https://github.com/nf-core/sarek/pull/1216) - Better test coverage for variant calling `*_all` subworkflows
- [#1217](https://github.com/nf-core/sarek/pull/1217) - Fix `groupTuple` statement for mutect2 tumor_only subworkflows
- [#1220](https://github.com/nf-core/sarek/pull/1220) - Fix channel and meta logic for `joint_mutect2` feature
- [#1221](https://github.com/nf-core/sarek/pull/1221) - Remove `lane` meta field after samplesheet validation to ensure proper merging after mapping
- [#1222](https://github.com/nf-core/sarek/pull/1222) - Better documentation for annotation cache
- [#1224](https://github.com/nf-core/sarek/pull/1224) - Update BCFTOOLS_SORT module with `--temp-dir .` added as option, which was required for Singularity
- [#1225](https://github.com/nf-core/sarek/pull/1225) - Better test coverage for all tests
- [#1227](https://github.com/nf-core/sarek/pull/1227) - Lint warning fix
- [#1229](https://github.com/nf-core/sarek/pull/1229) - Fix md5sum for gatk4_spark tests
- [#1230](https://github.com/nf-core/sarek/pull/1230) - Fix md5sum for sentieon aligner tests

### Dependencies

| Dependency    | Old version               | New version              |
| ------------- | ------------------------- | ------------------------ |
| `cnvkit`      | 0.9.9 (`samtools` 1.16.1) | 0.9.10 (`samtools` 1.17) |
| `ensembl-vep` | 108                       | 110                      |
| `grep`        | 3.4                       | 3.11                     |
| `multiqc`     | 1.14                      | 1.15                     |
| `tiddit`      | 3.3.2                     | 3.6.1                    |

## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare

Gällivare is a small lake next to Pierikjaure.

### Added

- [#1112](https://github.com/nf-core/sarek/pull/1112) - Back to dev
- [#1119](https://github.com/nf-core/sarek/pull/1119) - Added `help_text` for `input_output_options` group in schema
- [#1044](https://github.com/nf-core/sarek/pull/1044) - Adding support for several tools from Sentieon's DNAseq package. The standard fastq-to-vcf processing can now be done using Sentieon's DNAseq tools `ApplyVarCal`, `bwa mem`, `Dedup`, `GVCFtyper`, `Haplotyper`, `LocusCollector` and `VarCal`

### Changed

- [#1119](https://github.com/nf-core/sarek/pull/1119) - Remove `null` by default in schema
- [#1128](https://github.com/nf-core/sarek/pull/1128) - Prepare release `3.2.3`

### Fixed

- [#1118](https://github.com/nf-core/sarek/pull/1118) - Remove `public_aws_ecr` profile

## [3.2.2](https://github.com/nf-core/sarek/releases/tag/3.2.2) - Vuoinesluobbalah

Vuoinesluobbalah is a lake close to Bierikjávrre.

### Added

- [#1106](https://github.com/nf-core/sarek/pull/1106) - Add Slack integration to Megatests
- [#1107](https://github.com/nf-core/sarek/pull/1107) - Add `singularity.registry` to `public_aws_ecr`

### Changed

- [#1087](https://github.com/nf-core/sarek/pull/1087) - Back to dev
- [#1087](https://github.com/nf-core/sarek/pull/1087) - Minor modules update
- [#1088](https://github.com/nf-core/sarek/pull/1088) - Replace profile `test` by `test_cache` and add a `test` profile without hidden files
- [#1095](https://github.com/nf-core/sarek/pull/1095) - Prepare release `3.2.2`

### Fixed

- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in `GATK4_CREATESEQUENCEDICTIONARY` [#1085](https://github.com/nf-core/sarek/pull/1085)
- [#1089](https://github.com/nf-core/sarek/pull/1089) - Remove duplicated code
- [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName
- [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094)
- [#1100](https://github.com/nf-core/sarek/pull/1100) - Remove duplicate index with deepvariant when no_intervals [#1069](https://github.com/nf-core/sarek/pull/1069)
- [#1101](https://github.com/nf-core/sarek/pull/1101) - Remove duplicate index computation for GATK4 Markduplicates & [#1065](https://github.com/nf-core/sarek/issues/1065)
- [#1101](https://github.com/nf-core/sarek/pull/1101) - Fix GATK4 version for GATK4 MarkduplicatesSpark [#1068](https://github.com/nf-core/sarek/issues/1068)
- [#1105](https://github.com/nf-core/sarek/pull/1105) - Remove `params.tracedir`
- [#1108](https://github.com/nf-core/sarek/pull/1108) - Refactor bad prefix definition for vcf files [#938](https://github.com/nf-core/sarek/issues/938)
- [#1109](https://github.com/nf-core/sarek/pull/1109) - Fix `mpileup` for variantcalling: only `bcftools` run and file publishing

## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure

Pierikjaure is a previous spelling of Bierikjávrre.

### Changed

- [#1073](https://github.com/nf-core/sarek/pull/1073) - Back to dev
- [#1080](https://github.com/nf-core/sarek/pull/1080) - Prepare release `3.2.1`
- [#1082](https://github.com/nf-core/sarek/pull/1082) - Bump minimal Nextflow version to 23.04.0

### Fixed

- [#1078](https://github.com/nf-core/sarek/pull/1078) - Update tabix/bgziptabix module to fix typo
- [#1079](https://github.com/nf-core/sarek/pull/1079) - Fixed typo in profile name for tower aws megatests
- [#1082](https://github.com/nf-core/sarek/pull/1082) - Patch more modules to use quay.io registry
- [#1082](https://github.com/nf-core/sarek/pull/1082) - Update `public_aws_ecr` profile
- [#1082](https://github.com/nf-core/sarek/pull/1082) - Add quay.io as singularity default registry

## [3.2.0](https://github.com/nf-core/sarek/releases/tag/3.2.0) - Bierikjávrre

Bierikjávrre is one of the largest lake in Sarek.

### Added

- [#864](https://github.com/nf-core/sarek/pull/864) - Added possibilities to export assembled haplotypes and locally realigned reads
- [#792](https://github.com/nf-core/sarek/pull/792) - Added the option `--concatenate_vcfs` for concatenating the germline VCF files. Per default, the resulting vcf-files will be placed under `<outDir>/variant_calling/concat`
- [#889](https://github.com/nf-core/sarek/pull/889) - Added possibilities to skip variant filtering after Haplotypecaller
- [#945](https://github.com/nf-core/sarek/pull/945) - Adding Adam Talbot to contributor list
- [#954](https://github.com/nf-core/sarek/pull/954) - Adding keys for annotation with snpeff and ensemblvep for `hg19`, `hg38` and `mm10`
- [#967](https://github.com/nf-core/sarek/pull/967) - Adding new `outdir_cache` params
- [#971](https://github.com/nf-core/sarek/pull/971) - Subtle bugfix to correct mutation of FASTP output channel objects
- [#978](https://github.com/nf-core/sarek/pull/978) - Validate that patient/sample does not contain spaces
- [#981](https://github.com/nf-core/sarek/pull/981) - Added documentation on generating ASCAT resources for exome and targeted sequencing
- [#1041](https://github.com/nf-core/sarek/pull/1041) - Add params `vep_custom_args` to let user specify custom params more easily for `VEP`
- [#1045](https://github.com/nf-core/sarek/pull/1045) - Add `public_aws_ecr` for using ECR hosted containers

### Changed

- [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev
- [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - `vcf_annotate_snpeff`
- [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - `vcf_annotate_ensemblvep`
- [#874](https://github.com/nf-core/sarek/pull/874) - Update all modules
- [#882](https://github.com/nf-core/sarek/pull/882) - Remove exit strategy for `Manta`/`Strelka`
- [#890](https://github.com/nf-core/sarek/pull/890) - Sync `TEMPLATE` with `tools` `2.7.1`
- [#896](https://github.com/nf-core/sarek/pull/896) - Code refactoring
- [#898](https://github.com/nf-core/sarek/pull/898) - Nextflow minimal version is now `22.10.1`
- [#898](https://github.com/nf-core/sarek/pull/898) - Sync `TEMPLATE` with `tools` `2.7.2`
- [#909](https://github.com/nf-core/sarek/pull/909) - Cache test data on GHA
- [#928](https://github.com/nf-core/sarek/pull/928) - No need for BAI when starting from uBAM
- [#935](https://github.com/nf-core/sarek/pull/935) - Add params `build_only_index` to only build index
- [#936](https://github.com/nf-core/sarek/pull/936) - Add params `donwload_cache` to download annotation cache
- [#942](https://github.com/nf-core/sarek/pull/942) - Update `README.md`
- [#967](https://github.com/nf-core/sarek/pull/967) - Update and detail extensively how to use annotation cache
- [#968](https://github.com/nf-core/sarek/pull/968) - Update all modules
- [#1011](https://github.com/nf-core/sarek/pull/1011) - Sync `TEMPLATE` with `tools` `2.8`
- [#1012](https://github.com/nf-core/sarek/pull/1012) - Better handling of meta maps in `bam_variant_calling_somatic_mutect2`
- [#1014](https://github.com/nf-core/sarek/pull/1014) - `snpeff_db` is now only the `db` version and not `genome.db`
- [#1015](https://github.com/nf-core/sarek/pull/1015) - Increase default value for `--nucleotides_per_second` to `200000` resulting in 21 groups for `GATK.GRCh38`
- [#1019](https://github.com/nf-core/sarek/pull/1019) - Set a default registry outside of profile scope
- [#1031](https://github.com/nf-core/sarek/pull/1031) - Update pipeline summary
- [#1032](https://github.com/nf-core/sarek/pull/1032) - Update all modules
- [#1051](https://github.com/nf-core/sarek/pull/1051) - Update more modules
- [#1056](https://github.com/nf-core/sarek/pull/1056) - Bump pipeline version to `3.2.0`

### Fixed

- [#870](https://github.com/nf-core/sarek/pull/870) - Fix output for locally realigned reads from haplotypecaller
- [#874](https://github.com/nf-core/sarek/pull/874) - Remove `CITATION.cff`
- [#893](https://github.com/nf-core/sarek/pull/893) - Fix logic of when to execute tabix on dbsnp
- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to `--cnvkit_reference`
- [#894](https://github.com/nf-core/sarek/pull/894) - Remove methods description TODO prompt
- [#927](https://github.com/nf-core/sarek/pull/927) - Fix tumor only variant calling issues with freebayes following [#896](https://github.com/nf-core/sarek/pull/896)
- [#928](https://github.com/nf-core/sarek/pull/928) - Fix [#700](https://github.com/nf-core/sarek/issues/700)
- [#929](https://github.com/nf-core/sarek/pull/929) - Fix somatic variant calling issues with msisensor following [#896](https://github.com/nf-core/sarek/pull/896)
- [#941](https://github.com/nf-core/sarek/pull/941) - Fix json validation for `tools`, `skip_tools` and `use_gatk_spark` [#892](https://github.com/nf-core/sarek/issues/892)
- [#954](https://github.com/nf-core/sarek/pull/954) - Fix missing annotation keys with `snpeff` and `ensemblvep` for `hg19`
- [#957](https://github.com/nf-core/sarek/pull/957) - Add `failOnDuplicate` and `failOnMismatch` options to all `join()` operator where it was possible
- [#982](https://github.com/nf-core/sarek/pull/982) - Remove usage of exit statements, using `Nextflow.error` instead
- [#985](https://github.com/nf-core/sarek/pull/985) - Cache correctly identifies when it needs to be updated
- [#988](https://github.com/nf-core/sarek/pull/988) - Updated ascat module to fix seed for reproducibility
- [#998](https://github.com/nf-core/sarek/pull/998) - Remove parallelization within a sample for `Manta`
- [#1014](https://github.com/nf-core/sarek/pull/1014) - Fix calls to `ensemblvep` and `snpeff` containers
- [#1022](https://github.com/nf-core/sarek/pull/1022) - Fix call to variantrecalibrator. (Making sure that dbsnp_vqsr, known_indels_vqsr and known_snps_vqsr are channels, and not strings.)
- [#1039](https://github.com/nf-core/sarek/pull/1039) - Remove concatenate_vcfs tests with singularity, as they are failing due to not enough space on GHA runners
- [#1040](https://github.com/nf-core/sarek/pull/1040) - Fix dict channel issue due to [#1032](https://github.com/nf-core/sarek/pull/1032)
- [#1043](https://github.com/nf-core/sarek/pull/1043) - Fix typo in the tags.yml files from [#978](https://github.com/nf-core/sarek/pull/978)
- [#1048](https://github.com/nf-core/sarek/pull/1048) - Skip tool validation on annotation to fix [#949](https://github.com/nf-core/sarek/issues/949), check that bam is bam and cram is cram [#895](https://github.com/nf-core/sarek/issues/895)
- [#1050](https://github.com/nf-core/sarek/pull/1050) - Disable GATK VCF filters when joint calling to fix [#1025](https://github.com/nf-core/sarek/issues/1025)
- [#1055](https://github.com/nf-core/sarek/pull/1055) - Fix pattern for fasta file in the json schema
- [#1058](https://github.com/nf-core/sarek/pull/1058) - Fix container declaration for VCFTOOLS as it has been updated in the registry
- [#1061](https://github.com/nf-core/sarek/pull/1061) - Fix GenomicsDB also works with one interval file, fix results publishing of GenomicsDB
- [#1062](https://github.com/nf-core/sarek/pull/1062) - Fix automatic restart from steps
- [#1063](https://github.com/nf-core/sarek/pull/1063) - Fix join duplication for manta/strelka

### Removed

- [#898](https://github.com/nf-core/sarek/pull/898) - Params `enable_conda` was removed
- [#1070](https://github.com/nf-core/sarek/pull/1070) - Remove Sarek version from workflow and subway map pictures

### Dependencies

| Dependency    | Old version | New version |
| ------------- | ----------- | ----------- |
| `ascat`       | 3.0.0       | 3.1.1       |
| `bcftools`    | 1.15.1      | 1.17        |
| `deepvariant` | 1.4.0       | 1.5.0       |
| `ensembl-vep` | 106.1       | 108.2       |
| `fastp`       | 0.23.2      | 0.23.4      |
| `multiqc`     | 1.13a       | 1.14        |
| `samtools`    | 1.16        | 1.17        |
| `svdb`        | 2.6.1       | 2.8.1       |

### Modules / Subworkflows

| script                | Old name     | New name              |
| --------------------- | ------------ | --------------------- |
| `ensemblvep/download` |              | 'ENSEMBLVEP_DOWNLOAD' |
| `ensemblvep/vep`      | 'ENSEMBLVEP' | 'ENSEMBLVEP_VEP'      |
| `snpeff/download`     |              | 'SNPEFF_DOWNLOAD'     |
| `snpeff/snpeff`       | 'SNPEFF'     | 'SNPEFF_SNPEFF'       |

## [3.1.2](https://github.com/nf-core/sarek/releases/tag/3.1.2) - Lesser Lule River

Lesser Lule River is English for Lilla Luleälven

### Added

### Changed

### Fixed

- [#906](https://github.com/nf-core/sarek/pull/906) - Remove usages of deprecated `Channel.from` method

### Deprecated

### Removed

### Dependencies

## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven

Lilla Luleälven river's main affluent is Rapaätno.

### Added

- [#856](https://github.com/nf-core/sarek/pull/856) - Add annotation for `R64-1-1` and `UMD3.1`

### Changed

- [#855](https://github.com/nf-core/sarek/pull/855) - Speed up duplicate marking by using `samtools` for CRAM conversion
- [#858](https://github.com/nf-core/sarek/pull/858) - Prepare release `3.1.1`

### Fixed

- [#851](https://github.com/nf-core/sarek/pull/851) - Fix `schema` definition `None` for `cf_chrom_len`

### Deprecated

### Removed

### Dependencies

## [3.1](https://github.com/nf-core/sarek/releases/tag/3.1) - Rapaätno

Rapaätno is the river you can see from the Skierfe mountain.

### Added

- [#735](https://github.com/nf-core/sarek/pull/735) - GATK Markduplicates now natively supports CRAM output
- [#774](https://github.com/nf-core/sarek/pull/774) - Add logo for Danish National Genome Center
- [#783](https://github.com/nf-core/sarek/pull/783) - Add paths for chr length used by controlfreec to GRCh38 config
- [#820](https://github.com/nf-core/sarek/pull/820) - Improve documentation on scatter/gather effects
- [#833](https://github.com/nf-core/sarek/pull/833) - Add name to CI tests to avoid confusion between runs

### Changed

- [#735](https://github.com/nf-core/sarek/pull/735) - `--save_mapped` now saves mapping output in CRAM format
- [#762](https://github.com/nf-core/sarek/pull/762) - Back to dev
- [#762](https://github.com/nf-core/sarek/pull/762) - Update deepvariant module
- [#773](https://github.com/nf-core/sarek/pull/773) - Sync `TEMPLATE` with `tools` `2.6`
- [#782](https://github.com/nf-core/sarek/pull/782) - Reduce scatter/gather for full size tests on AWS
- [#785](https://github.com/nf-core/sarek/pull/785) - Update description of `bcftools stats`
- [#784](https://github.com/nf-core/sarek/pull/784) - Update all subworkflows names thanks to @scorreard
- [#806](https://github.com/nf-core/sarek/pull/806) - Refactor all tests
- [#806](https://github.com/nf-core/sarek/pull/806) - Split up `modules.config` file
- [#810](https://github.com/nf-core/sarek/pull/810) - Update CHANGELOG
- [#821](https://github.com/nf-core/sarek/pull/821) - Change `replace` to `putIfAbsent` for automatic search of `input` if none is provided to avoid overwriting values
- [#822](https://github.com/nf-core/sarek/pull/822) - Update modules with `nf-core modules update -a`: Update GATK version to 4.3.0
- [#827](https://github.com/nf-core/sarek/pull/827) - Add `--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader` to `GenomicsDB` parameters to speed up the analysis
- [#842](https://github.com/nf-core/sarek/pull/842) - Increase default memory for samtools stats
- [#844](https://github.com/nf-core/sarek/pull/844) - All small scale tests are run on PR to `master`

### Fixed

- [#762](https://github.com/nf-core/sarek/pull/762) - Polish CHANGELOG + figures
- [#766](https://github.com/nf-core/sarek/pull/766) - Align box description in subway map
- [#768](https://github.com/nf-core/sarek/pull/768) - Use double quotes to fix import of singularity images for deepvariant module
- [#770](https://github.com/nf-core/sarek/pull/770) - Use double quotes to fix import of singularity images for gatk4/cnnscorevariants module
- [#771](https://github.com/nf-core/sarek/pull/771) - update to new modules syntax
- [#777](https://github.com/nf-core/sarek/pull/777) - Fix mixed up aws full size tests output paths
- [#790](https://github.com/nf-core/sarek/pull/790) - Fix issue [#789](https://github.com/nf-core/sarek/issues/789) somatic mutect2 test
- [#793](https://github.com/nf-core/sarek/pull/793) - Remove DeepVariant GVCF from annotation
- [#794](https://github.com/nf-core/sarek/pull/794) - Fix publishing for unzipped reference files
- [#807](https://github.com/nf-core/sarek/pull/807) - Fix read group when uBAMs are provided (see issue [#732](https://github.com/nf-core/sarek/issues/732))
- [#813](https://github.com/nf-core/sarek/pull/813) - Fix input validation when launching from website (see issue [#694](https://github.com/nf-core/sarek/issues/694))
- [#814](https://github.com/nf-core/sarek/pull/814) - Fix readgroups when using DragMap together with FreeBayes or Mutect2 (see issue [#780](https://github.com/nf-core/sarek/issues/780))
- [#817](https://github.com/nf-core/sarek/pull/817) - Fix CNVKit run on tumor-only sample to be run on all samples
- [#828](https://github.com/nf-core/sarek/pull/817) - Fix issue [#763](https://github.com/nf-core/sarek/issues/763) to run variantcalling when starting form step recalibration
- [#837](https://github.com/nf-core/sarek/pull/837) - Fix Freebayes config selector after subworkflow renaming
- [#839](https://github.com/nf-core/sarek/pull/839) - Remove `copyTo` method that fails on S3 when the source and destination buckets are in different regions
- [#841](https://github.com/nf-core/sarek/pull/841) - Fix path priority for `cf_chrom_len`

### Deprecated

### Removed

### Dependencies

| Dependency    | Old version | New version |
| ------------- | ----------- | ----------- |
| `bcftools`    | 1.15.1      | 1.16        |
| `deepvariant` | 1.3.0       | 1.4.0       |
| `freebayes`   | 1.3.5       | 1.3.6       |
| `gatk4`       | 4.2.6.1     | 4.3.0.0     |
| `samtools`    | 1.15.1      | 1.16.1      |
| `tiddit`      | 3.1.0       | 3.3.2       |

## [3.0.2](https://github.com/nf-core/sarek/releases/tag/3.0.2) - Lájtávrre

Lájtávrre is a lake you can see from the Skierfe mountain, formed by the Rapaätno river.

### Added

- [#691](https://github.com/nf-core/sarek/pull/691) - Enable `PROFILE=conda`, `PROFILE=docker` and `PROFILE=singularity` for pytest
- [#716](https://github.com/nf-core/sarek/pull/716) - Add documentation for Azure recommended config vm_size
- [#752](https://github.com/nf-core/sarek/pull/752) - Add tracking of all dependencies starting 3.0

### Changed

- [#679](https://github.com/nf-core/sarek/pull/679) - Back to `dev`
- [#685](https://github.com/nf-core/sarek/pull/685) - Updating the nf-core modules used by Sarek
- [#691](https://github.com/nf-core/sarek/pull/691) - To run the same pytest as before locally, use `PROFILE=docker`
- [#692](https://github.com/nf-core/sarek/pull/692) - Use `params.tools=strelka` in profile `test`
- [#696](https://github.com/nf-core/sarek/pull/696) - Adding check of md5-sums in CI-tests
- [#719](https://github.com/nf-core/sarek/pull/719) - Added boxes to subway map
- [#720](https://github.com/nf-core/sarek/pull/720) - Sync `TEMPLATE` with `tools` `2.5`
- [#723](https://github.com/nf-core/sarek/pull/723) - Sync `TEMPLATE` with `tools` `2.5.1`
- [#726](https://github.com/nf-core/sarek/pull/726) - Adapt resource requests
- [#730](https://github.com/nf-core/sarek/pull/730) - Reduce number of tests
- [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_germline`
- [#733](https://github.com/nf-core/sarek/pull/733) - Add description for params.cf_chrom_len
- [#734](https://github.com/nf-core/sarek/pull/734) - nf-core modules update -a
- [#736](https://github.com/nf-core/sarek/pull/736) - More extensive CI for default test
- [#742](https://github.com/nf-core/sarek/pull/742) - Requiring the Haplotypecaller to be specified as one of the tools for joint germline genotyping
- [#752](https://github.com/nf-core/sarek/pull/752) - Code polishing

### Fixed

- [#679](https://github.com/nf-core/sarek/pull/679) - Fixed typos in subway maps
- [#681](https://github.com/nf-core/sarek/pull/681) - Fixed intermediate files published cf [#680](https://github.com/nf-core/sarek/issues/680)
- [#688](https://github.com/nf-core/sarek/pull/688) - Fixed VEP plugins issue cf [#687](https://github.com/nf-core/sarek/issues/687)
- [#689](https://github.com/nf-core/sarek/pull/689) - Fixed when clause for non `BWA mem` building mapping indexes
- [#704](https://github.com/nf-core/sarek/pull/704) - Fixed `cf_ploidy` to string instead of number
- [#705](https://github.com/nf-core/sarek/pull/705) - Fix publishing for processes in `alignment_to_fastq` subworkflow; prevent tabix computation for `known_snps` when present; publish `umi` processed files into `preprocessing/umi` subdirectory
- [#706](https://github.com/nf-core/sarek/pull/706) - Fixed `vep_version` not found error when running `--vep_loftee`
- [#724](https://github.com/nf-core/sarek/pull/724) - Fixed prettier issue
- [#727](https://github.com/nf-core/sarek/pull/727) - Allow `.list` interval files; remove `seconds` from GRCh38 file to allow `--nucleotides_per_second` to be used
- [#728](https://github.com/nf-core/sarek/pull/728) - Circumvent issue with controlfreec and length file containing regions not in intervals file
- [#729](https://github.com/nf-core/sarek/pull/729) - Trailing commas in `--tools`, `--skip_tools` and `--use_gatk_spark` now raise failure cf [#722](https://github.com/nf-core/sarek/issues/722)
- [#741](https://github.com/nf-core/sarek/pull/741) - Fix prefix for `bcftools sort` for joint germline variant calling
- [#743](https://github.com/nf-core/sarek/pull/743) - Remove profile definitions in profile to avoid issues with Tower
- [#758](https://github.com/nf-core/sarek/pull/758) - Fix Zenodo batch
- [#760](https://github.com/nf-core/sarek/pull/760) - Fix CHANGELOG dependencies
- [#761](https://github.com/nf-core/sarek/pull/761) - Fix font in subway map and workflow image

### Deprecated

### Removed

- [#742](https://github.com/nf-core/sarek/pull/742) - Removed some lines from the usage-doc as Sarek no longer support input supplied as a list of multiple csv-files
- [#757](https://github.com/nf-core/sarek/pull/757) - Remove `errorStrategy` in `conf/modules.config`

## [3.0.1](https://github.com/nf-core/sarek/releases/tag/3.0.1) - Saiva

Saiva is a lake in the Sarek national park, just below the Skierfe mountain.

### Fixed

- [#708](https://github.com/nf-core/sarek/pull/708) - Fixes mpileup bug. Update nf-core module `samtools/mpileup` to subset CRAM file by intervals

## [3.0](https://github.com/nf-core/sarek/releases/tag/3.0) - Skierfe

Skierfe is a mountain in the Sarek national park, and the inspiration for the logo.

### Added

- [#388](https://github.com/nf-core/sarek/pull/388) - Add cram support + read splitting with `SeqKit` for speedup
- [#394](https://github.com/nf-core/sarek/pull/394) - Add `DeepVariant`
- [#411](https://github.com/nf-core/sarek/pull/411) - cram in csv samplesheet
- [#448](https://github.com/nf-core/sarek/pull/448) - Allow to skip base quality recalibration with `--skip_bqsr`
- [#449](https://github.com/nf-core/sarek/pull/449) - [@FriederikeHanssen](https://github.com/FriederikeHanssen) is now a `CODEOWNERS`
- [#460](https://github.com/nf-core/sarek/pull/460) - Add posters
- [#463](https://github.com/nf-core/sarek/pull/463) - Add dark/light logo versions
- [#464](https://github.com/nf-core/sarek/pull/464), [#514](https://github.com/nf-core/sarek/pull/514) - Add `DRAGMAP` as a possible aligner
- [#479](https://github.com/nf-core/sarek/pull/479) - Add more subworkflows
- [#485](https://github.com/nf-core/sarek/pull/485) - `--skip_qc`, `--skip_markduplicates` and `--skip_bqsr` is now `--skip_tools`
- [#507](https://github.com/nf-core/sarek/pull/507), [#537](https://github.com/nf-core/sarek/pull/537) - Subway map for building indexes
- [#512](https://github.com/nf-core/sarek/pull/512), [#531](https://github.com/nf-core/sarek/pull/531), [#537](https://github.com/nf-core/sarek/pull/537) - Subway map for pipeline
- [#522](https://github.com/nf-core/sarek/pull/522) - Add QC for vcf files & MultiQC
- [#533](https://github.com/nf-core/sarek/pull/533) - Add param `--only_paired_variant_calling` to allow skipping of germline variantcalling for paired samples
- [#536](https://github.com/nf-core/sarek/pull/536) - Add `--step markduplicates` to start from duplicate marking, `--step prepare_recalibration` now ONLY starts at process `BaseRecalibrator` & adding `bam` and `cram` input support for `--step` `markduplicates`, `prepare_recalibration`, `recalibrate`, and `variant_calling`
- [#538](https://github.com/nf-core/sarek/pull/538) - Add param `--seq_platform`, default: `ILLUMINA`
- [#545](https://github.com/nf-core/sarek/pull/545) - Add modules and subworkflows for `cnvkit` tumor_only mode
- [#540](https://github.com/nf-core/sarek/pull/540) - Add modules and subworkflows for `cnvkit` somatic mode
- [#557](https://github.com/nf-core/sarek/pull/557) - Add `Haplotypecaller` single sample mode together with `CNNScoreVariants` and `FilterVariantTranches`
- [#576](https://github.com/nf-core/sarek/pull/576) - Add modules and subworkflows for `cnvkit` germline mode
- [#582](https://github.com/nf-core/sarek/pull/582) - Added option `--vep_out_format` for setting the format of the output-file from VEP to `json`, `tab` or `vcf` (default)
- [#594](https://github.com/nf-core/sarek/pull/594) - Add parameter `--save_output_as_bam` to allow output of result files in BAM format
- [#595](https://github.com/nf-core/sarek/pull/595) - Added Haplotypecaller joint germline calling
- [#597](https://github.com/nf-core/sarek/pull/597) - Added tiddit for tumor variant calling
- [#600](https://github.com/nf-core/sarek/pull/600) - Added description for UMI related params in schema
- [#604](https://github.com/nf-core/sarek/pull/604), [#617](https://github.com/nf-core/sarek/pull/617) - Added full size tests WGS 30x NA12878
- [#613](https://github.com/nf-core/sarek/pull/613) - Added params `--dbnsfp_fields` to allow configuration of fields for the `dbnsfp` `VEP` plugin
- [#613](https://github.com/nf-core/sarek/pull/613) - Added params `--dbnsfp_consequence` to allow configuration of consequence for the `dbnsfp` `VEP` plugin
- [#613](https://github.com/nf-core/sarek/pull/613) - Added params `--vep_version` to allow more configuration on the vep container definition
- [#620](https://github.com/nf-core/sarek/pull/620) - Added checks for sex information when running a CNV tools
- [#623](https://github.com/nf-core/sarek/pull/623) - Additional checks of data in the input sample sheet
- [#629](https://github.com/nf-core/sarek/pull/629) - Added checks to catch inconsistency between supplied samples and requested tools
- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--snpeff_version` to allow more configuration on the snpeff container definition
- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--vep_include_fasta` to use the fasta file for annotation
- [#639](https://github.com/nf-core/sarek/pull/639) - Adding genes-txt-file and summary-html-file to the published output from snpEff
- [#647](https://github.com/nf-core/sarek/pull/647) - Update resource requests for preprocessing based on what worked for 5 ICGC matched WGS samples
- [#652](https://github.com/nf-core/sarek/pull/652) - Added full size somatic test profile

### Changed

- [#580](https://github.com/nf-core/sarek/pull/580) - changed the test_full config to real public WXS data. 1 sample WXS germline, 1 Tumor/Normal pair. https://doi.org/10.1038/sdata.2016.25 and https://doi.org/10.1038/s41587-021-00994-5
- [#383](https://github.com/nf-core/sarek/pull/383), [#528](https://github.com/nf-core/sarek/pull/528) - Update `CHANGELOG`
- [#390](https://github.com/nf-core/sarek/pull/390) - Update `nextflow_schema.json`
- [#408](https://github.com/nf-core/sarek/pull/408) - Sync `TEMPLATE` with `tools` `2.0.1`
- [#416](https://github.com/nf-core/sarek/pull/416) - Sync `TEMPLATE` with `tools` `2.1`
- [#417](https://github.com/nf-core/sarek/pull/417) - Merge `dsl2` and `dev` branches
- [#419](https://github.com/nf-core/sarek/pull/419) - Improve preprocessing
- [#420](https://github.com/nf-core/sarek/pull/420), [#455](https://github.com/nf-core/sarek/pull/455), [#459](https://github.com/nf-core/sarek/pull/459), [#633](https://github.com/nf-core/sarek/pull/633) - `nf-core modules update --all`
- [#427](https://github.com/nf-core/sarek/pull/427) - Update `DeepVariant`
- [#462](https://github.com/nf-core/sarek/pull/462) - Update modules and `modules.config`
- [#465](https://github.com/nf-core/sarek/pull/465) - Improve `test_data.config`
- [#466](https://github.com/nf-core/sarek/pull/466), [#478](https://github.com/nf-core/sarek/pull/478), [#492](https://github.com/nf-core/sarek/pull/492), [#521](https://github.com/nf-core/sarek/pull/521) - Move some local modules to `nf-core/modules`
- [#466](https://github.com/nf-core/sarek/pull/466), [#485](https://github.com/nf-core/sarek/pull/485), [#492](https://github.com/nf-core/sarek/pull/492), [#494](https://github.com/nf-core/sarek/pull/494), [#515](https://github.com/nf-core/sarek/pull/515) - Improve preprocessing subworkflows
- [#474](https://github.com/nf-core/sarek/pull/474), [#475](https://github.com/nf-core/sarek/pull/475) - Sync `TEMPLATE` with `tools` `2.2`
- [#487](https://github.com/nf-core/sarek/pull/487), [#489](https://github.com/nf-core/sarek/pull/489), [#492](https://github.com/nf-core/sarek/pull/492), [#497](https://github.com/nf-core/sarek/pull/497), [#522](https://github.com/nf-core/sarek/pull/522), [#583](https://github.com/nf-core/sarek/pull/583) - Improve variant calling subworkflows
- [#498](https://github.com/nf-core/sarek/pull/498) - Update docs
- [#501](https://github.com/nf-core/sarek/pull/501) - Sync `TEMPLATE` with `tools` `2.3`
- [#511](https://github.com/nf-core/sarek/pull/511) - Sync `TEMPLATE` with `tools` `2.3.2`
- [#520](https://github.com/nf-core/sarek/pull/520) - Improve annotation subworkflows
- [#537](https://github.com/nf-core/sarek/pull/537) - Update workflow figure
- [#539](https://github.com/nf-core/sarek/pull/539) - Update `CITATIONS.md`
- [#544](https://github.com/nf-core/sarek/pull/544) - `Mutect2` is no longer compatible with `--no_intervals`
- [#551](https://github.com/nf-core/sarek/pull/551) - Sync `TEMPLATE` with `tools` `2.4`
- [#562](https://github.com/nf-core/sarek/pull/562) - Restart from `--step annotate` is now also requiring a CSV file
- [#563](https://github.com/nf-core/sarek/pull/563) - Updated subway map
- [#570](https://github.com/nf-core/sarek/pull/570) - Extract mpileup into its own subworkflow; zip mpileup files
- [#571](https://github.com/nf-core/sarek/pull/571) - Including and using GATK4's mergeVcfs
- [#572](https://github.com/nf-core/sarek/pull/572) - Adjusted subway map svg for firefox compatibility
- [#577](https://github.com/nf-core/sarek/pull/577) - Update `RELEASE_CHECKLIST`
- [#578](https://github.com/nf-core/sarek/pull/578) - Updated module deeptools/bamcoverage
- [#585](https://github.com/nf-core/sarek/pull/585) - Remove explicit BAM to CRAM conversion after MarkduplicatesSpark; tool does it internally
- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`
- [#593](https://github.com/nf-core/sarek/pull/593) - update `ensembl-vep` cache version and module
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `TODO` in awsfulltest
- [#606](https://github.com/nf-core/sarek/pull/606) - Updated `ASCAT` to version `3.0` as module
- [#608](https://github.com/nf-core/sarek/pull/608) - Prevent candidate VCFs from getting published in manta
- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module
- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
- [#620](https://github.com/nf-core/sarek/pull/620) - `gender` is now `sex` in the samplesheet
- [#630](https://github.com/nf-core/sarek/pull/630) - Update citations file
- [#632](https://github.com/nf-core/sarek/pull/632) - Update `snpEff` version to `5.1` and cache up to `105`
- [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106`
- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
- [#633](https://github.com/nf-core/sarek/pull/633) - Update `BCFTOOLS` version to `1.15.1`
- [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
- [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
- [#646](https://github.com/nf-core/sarek/pull/646) - Update `nextflow_schema.json` to reflect new parameters and functions, removes `--annotation_cache`, removes `--ascat_chromosomes`
- [#649](https://github.com/nf-core/sarek/pull/649) - Update, simplify and add more files to all `test_*.yml` files
- [#651](https://github.com/nf-core/sarek/pull/651) - Added TIDDIT_SOMATIC subworkflow
- [#653](https://github.com/nf-core/sarek/pull/653) - Coherent results subfolder structure between preprocessing, variantcalling and reporting
- [#659](https://github.com/nf-core/sarek/pull/659) - Update usage.md docu section on `How to run ASCAT with WES`
- [#661](https://github.com/nf-core/sarek/pull/661) - Add cnvkit reference creation to index subway map
- [#662](https://github.com/nf-core/sarek/pull/662) - Add bgzipped and indexed GATKBundle reference files for `GATK.GRCh37` and replace germline-resources with GATKBundle one
- [#663](https://github.com/nf-core/sarek/pull/663) - Add separate parameters for `ASCAT` and `ControlFREEC` back in
- [#668](https://github.com/nf-core/sarek/pull/668) - Update annotation documentation
- [#674](https://github.com/nf-core/sarek/pull/664) - Default value for splitting is `50000000`

### Fixed

- [#234](https://github.com/nf-core/sarek/pull/234) - Switching to DSL2
- [#234](https://github.com/nf-core/sarek/pull/234), [#238](https://github.com/nf-core/sarek/pull/238) - Add modules and sub workflow for building indices
- [#234](https://github.com/nf-core/sarek/pull/234), [#252](https://github.com/nf-core/sarek/pull/252), [#256](https://github.com/nf-core/sarek/pull/256), [#283](https://github.com/nf-core/sarek/pull/283), [#334](https://github.com/nf-core/sarek/pull/334) - Update Nextflow `19.10.0` -> `20.11.0-edge`
- [#239](https://github.com/nf-core/sarek/pull/239) - Restore Sarek ascii art to header
- [#241](https://github.com/nf-core/sarek/pull/241), [#248](https://github.com/nf-core/sarek/pull/248), [#250](https://github.com/nf-core/sarek/pull/250), [#257](https://github.com/nf-core/sarek/pull/257), [#259](https://github.com/nf-core/sarek/pull/259) - Add modules and sub workflow for preprocessing
- [#242](https://github.com/nf-core/sarek/pull/242), [#244](https://github.com/nf-core/sarek/pull/244), [#245](https://github.com/nf-core/sarek/pull/245), [#246](https://github.com/nf-core/sarek/pull/246), [#247](https://github.com/nf-core/sarek/pull/247), [#249](https://github.com/nf-core/sarek/pull/249), [#252](https://github.com/nf-core/sarek/pull/252), [#256](https://github.com/nf-core/sarek/pull/256), [#263](https://github.com/nf-core/sarek/pull/263), [#264](https://github.com/nf-core/sarek/pull/264), [#283](https://github.com/nf-core/sarek/pull/283), [#285](https://github.com/nf-core/sarek/pull/285), [#338](https://github.com/nf-core/sarek/pull/338) - Refactor `dsl2` branch
- [#257](https://github.com/nf-core/sarek/pull/257) - Use a params modules config file
- [#266](https://github.com/nf-core/sarek/pull/266), [#285](https://github.com/nf-core/sarek/pull/285), [#297](https://github.com/nf-core/sarek/pull/297) - Add modules and sub workflow for variant calling
- [#333](https://github.com/nf-core/sarek/pull/333) - Bump `Sarek` version to `3.0dev`
- [#334](https://github.com/nf-core/sarek/pull/334) - Sync `dsl2` and `dev` branches
- [#342](https://github.com/nf-core/sarek/pull/342) - Update `README.md`
- [#386](https://github.com/nf-core/sarek/pull/386) - Annotation is back
- [#410](https://github.com/nf-core/sarek/pull/410), [#412](https://github.com/nf-core/sarek/pull/412), [#584](https://github.com/nf-core/sarek/pull/584) - Update `CI` tests
- [#418](https://github.com/nf-core/sarek/pull/418) - Fix `known_sites` channels
- [#432](https://github.com/nf-core/sarek/pull/432), [#457](https://github.com/nf-core/sarek/pull/457) - Sort before `tabix index`
- [#454](https://github.com/nf-core/sarek/pull/454) - Input is optional (can actually be found automatically by `Sarek` if previously run)
- [#463](https://github.com/nf-core/sarek/pull/463), [#468](https://github.com/nf-core/sarek/pull/468) - Fix `nf-core lint`
- [#513](https://github.com/nf-core/sarek/pull/513), [#527](https://github.com/nf-core/sarek/pull/527) - CNV is back
- [#529](https://github.com/nf-core/sarek/pull/529) - Do not save `versions.yml` files
- [#524](https://github.com/nf-core/sarek/pull/524) - Fix intervals usage by counting the actual list of scatter/gather files produced and not overall number of intervals
- [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with <https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339>
- [#567](https://github.com/nf-core/sarek/pull/567) - Fix interval name resolving during scatter/gather by moving logic to modules.config causing name to be correctly resolved on process execution; also fixed duplicate naming when variant callers produce multiple vcf files by adding field `type` to `meta` map
- [#585](https://github.com/nf-core/sarek/pull/585) - Fix Spark usage for GATK4 modules
- [#587](https://github.com/nf-core/sarek/pull/587) - Fix issue with VEP extra files
- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is back
- [#590](https://github.com/nf-core/sarek/pull/590) - Fix empty folders during scatter/gather
- [#592](https://github.com/nf-core/sarek/pull/592) - Fix optional resources for Mutect2, GetPileupSummaries, and HaplotypeCaller: issue [#299](https://github.com/nf-core/sarek/issues/299), [#359](https://github.com/nf-core/sarek/issues/359), [#367](https://github.com/nf-core/sarek/issues/367)
- [#598](https://github.com/nf-core/sarek/pull/598), [#614](https://github.com/nf-core/sarek/pull/614), [#626](https://github.com/nf-core/sarek/pull/626) - Remove WARNING message for config selector not matching
- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for correct data type for `params.step`
- [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for no empty `--tools` with `--step variant_calling` or `--step annotate`
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
- [#602](https://github.com/nf-core/sarek/pull/602) - Fixed bug in `alignment_to_fastq` and added tests
- [#609](https://github.com/nf-core/sarek/pull/609) - Remove unused intervals code, reorganize combined intervals file
- [#613](https://github.com/nf-core/sarek/pull/613) - Fixed filenames for `dbnsfp` and `SpliceAI` `VEP` plugin
- [#615](https://github.com/nf-core/sarek/pull/615) - Fix ASCAT igenomes file paths
- [#619](https://github.com/nf-core/sarek/pull/619) - Fix issue with checking samplesheet content with AWS
- [#628](https://github.com/nf-core/sarek/pull/628) - Fix issue with value converting to string before schema validation
- [#628](https://github.com/nf-core/sarek/pull/628) - Fix dbsnp check issue with `--step annotate`
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix `bcftools/vcftools` sample labelling in multiqc report
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix issue with tiddit [#621](https://github.com/nf-core/sarek/issues/621)
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix channel issue with `targets.bed` in prepare_intervals
- [#634](https://github.com/nf-core/sarek/pull/634) - Fix issue with samtools/mosdepth plots in multiqc_report
- [#641](https://github.com/nf-core/sarek/pull/641) - Fix issue with duplicate substring in tools and skip_tools
- [#642](https://github.com/nf-core/sarek/pull/642) - Only unzip ref files if tool is run, only publish ref files if `--save_reference` and simplify CNKit logic
- [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks
- [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files
- [#655](https://github.com/nf-core/sarek/pull/655) - Fix `--intervals false` logic & add versioning for local modules
- [#658](https://github.com/nf-core/sarek/pull/658) - Fix split fastq names in multiqc-report
- [#666](https://github.com/nf-core/sarek/pull/666) - Simplify multiqc config channel input
- [#668](https://github.com/nf-core/sarek/pull/668) - Add `snpeff_version` and `vep_version` to `schema_ignore_params` to avoid issue when specifying on command line
- [#669](https://github.com/nf-core/sarek/pull/669) - Fix path to files when creating csv files

### Dependencies

| Dependency             | Old version | New version |
| ---------------------- | ----------- | ----------- |
| `ascat`                | 2.5.2       | 3.0.0       |
| `bcftools`             | 1.9         | 1.15.1      |
| `bwa-mem2`             | 2.0         | 2.2.1       |
| `bwa`                  | 0.7.17      | unchanged   |
| `cancerit-allelecount` | 4.0.2       | 4.3.0       |
| `cnvkit`               | 0.9.6       | 0.9.9       |
| `control-freec`        | 11.6        | unchanged   |
| `deepvariant`          | added       | 1.3.0       |
| `dragmap`              | added       | 1.2.1       |
| `ensembl-vep`          | 99.2        | 106.1       |
| `fastp`                | added       | 0.23.2      |
| `fastqc`               | 0.11.9      | unchanged   |
| `fgbio`                | 1.1.0       | 2.0.2       |
| `freebayes`            | 1.3.2       | 1.3.5       |
| `gatk4`                | 4.1.7.0     | 4.2.6.1     |
| `gawk`                 | added       | 5.1.0       |
| `genesplicer`          | 1.0         | removed     |
| `htslib`               | 1.9         | removed     |
| `llvm-openmp`          | 8.0.1       | removed     |
| `manta`                | 1.6.0       | unchanged   |
| `markdown`             | 3.1.1       | removed     |
| `mosdepth`             | 0.3.3       | unchanged   |
| `msisensor-pro`        | 1.1.a       | 1.2.0       |
| `msisensor`            | 0.5         | removed     |
| `multiqc`              | 1.8         | 1.13a       |
| `openjdk`              | added       | 8.0.312     |
| `openmp`               | 8.0.1       | removed     |
| `p7zip`                | added       | 15.09       |
| `pigz`                 | 2.3.4       | unchanged   |
| `pygments`             | 2.5.2       | removed     |
| `pymdown-extensions`   | 6.0         | removed     |
| `qualimap`             | 2.2.2d      | removed     |
| `r-ggplot2`            | 3.3.0       | removed     |
| `samblaster`           | 0.1.24      | 0.1.26      |
| `samtools`             | 1.9         | 1.15.1      |
| `sed`                  | added       | 4.7         |
| `snpeff`               | 4.3.1t      | 5.1         |
| `strelka`              | 2.9.10      | unchanged   |
| `svdb`                 | added       | 2.6.1       |
| `tabix`                | added       | 1.11        |
| `tiddit`               | 2.7.1       | 3.1.0       |
| `trim-galore`          | 0.6.5       | removed     |
| `vcfanno`              | 0.3.2       | removed     |
| `vcftools`             | 0.1.16      | unchanged   |

### Deprecated

### Removed

- [#485](https://github.com/nf-core/sarek/pull/485) - `--skip_qc`, `--skip_markduplicates` and `--skip_bqsr` is now `--skip_tools`
- [#538](https://github.com/nf-core/sarek/pull/538) - `--sequencing_center` is now `--seq_center`
- [#538](https://github.com/nf-core/sarek/pull/538) - `--markdup_java_options` has been removed
- [#539](https://github.com/nf-core/sarek/pull/539) - `--annotate_tools` has been removed
- [#539](https://github.com/nf-core/sarek/pull/539) - `--cadd_cache`, `--cadd_indels`, `--cadd_indels_tbi`, `--cadd_wg_snvs`, `--cadd_wg_snvs_tbi` have been removed
- [#539](https://github.com/nf-core/sarek/pull/539) - `--genesplicer` has been removed
- [#539](https://github.com/nf-core/sarek/pull/539) - `conf/genomes.config` and `params.genomes_base` have been removed
- [#562](https://github.com/nf-core/sarek/pull/562) - Restart from `--step annotate` from folder is removed. Use a `csv` file instead
- [#571](https://github.com/nf-core/sarek/pull/571) - Removed the local module `concat_vcf`
- [#605](https://github.com/nf-core/sarek/pull/605) - Removed Scatter/gather from GATK_SINGLE_SAMPLE_GERMLINE_VARIANT_CALLING, all intervals are processed together
- [#643](https://github.com/nf-core/sarek/pull/643) - Removed Sentieon parameters

## [2.7.2](https://github.com/nf-core/sarek/releases/tag/2.7.2) - Áhkká

Áhkká is one of the massifs just outside of the Sarek National Park.

### Fixed

- [#566](https://github.com/nf-core/sarek/pull/566) - Fix caching bug affecting a variable number of `MapReads` jobs due to non-deterministic state of `statusMap` during caching evaluation

## [2.7.1](https://github.com/nf-core/sarek/releases/tag/2.7.1) - Pårtejekna

Pårtejekna is one of glaciers of the Pårte Massif.

### Added

- [#353](https://github.com/nf-core/sarek/pull/353) - Add support for task retries with exit code 247 (exhibited by `Picard MarkDuplicates`)
- [#354](https://github.com/nf-core/sarek/pull/354) - Add tumor only mode for `Mutect2` and `MSIsensor`
- [#356](https://github.com/nf-core/sarek/pull/356) - Add `--cf_contamination_adjustment` params to adjust contamination with `Control-FREEC`
- [#372](https://github.com/nf-core/sarek/pull/372) - Add `--cf_contamination` params to specify contamination value with `Control-FREEC`

### Changed

- [#373](https://github.com/nf-core/sarek/pull/373) - Sync `TEMPLATE` with `tools` 1.14
- [#376](https://github.com/nf-core/sarek/pull/376) - Better logo on Github dark Mode
- [#387](https://github.com/nf-core/sarek/pull/387) - Fix tables for TSV file content

### Fixed

- [#375](https://github.com/nf-core/sarek/pull/375), [#381](https://github.com/nf-core/sarek/pull/381), [#382](https://github.com/nf-core/sarek/pull/382), [#385](https://github.com/nf-core/sarek/pull/385) - Fix bugs due to `TEMPLATE` sync from [#373](https://github.com/nf-core/sarek/pull/373)
- [#378](https://github.com/nf-core/sarek/pull/378) - Fix `Spark` related issue due to `Docker` settings in `nextflow.config`

### Deprecated

### Removed

- [#368](https://github.com/nf-core/sarek/pull/368) - Remove social preview image to use GitHub OpenGraph

## [2.7](https://github.com/nf-core/sarek/releases/tag/2.7) - Pårte

Pårte is one of the main massif in the Sarek National Park.

### Added

- [#145](https://github.com/nf-core/sarek/pull/145) - Add `UMI annotation and consensus` functionality to `Sarek`
- [#230](https://github.com/nf-core/sarek/pull/230) - Add `ignore_soft_clipped_bases` option for `GATK Mutect2` [#218](https://github.com/nf-core/sarek/issues/218)
- [#253](https://github.com/nf-core/sarek/pull/253) - Add `UMI` `CI` testing
- [#262](https://github.com/nf-core/sarek/pull/262) - Add `nextflow_schema.json`
- [#237](https://github.com/nf-core/sarek/pull/237), [#282](https://github.com/nf-core/sarek/pull/282) - Add `--aligner` to choose between `bwa` and `bwa-mem2`
- [#294](https://github.com/nf-core/sarek/pull/294) - Add `Troubleshooting` section to `docs/usage.md`
- [#302](https://github.com/nf-core/sarek/pull/302), [#304](https://github.com/nf-core/sarek/pull/304) - Add WES and tumor-only mode for `Control-FREEC`

### Changed

- [#253](https://github.com/nf-core/sarek/pull/253), [#255](https://github.com/nf-core/sarek/pull/255), [#326](https://github.com/nf-core/sarek/pull/326), [#329](https://github.com/nf-core/sarek/pull/329) - Update docs
- [#260](https://github.com/nf-core/sarek/pull/260), [#262](https://github.com/nf-core/sarek/pull/262), [#278](https://github.com/nf-core/sarek/pull/278), [#322](https://github.com/nf-core/sarek/pull/322) - Sync with `TEMPLATE` updated from [nf-core/tools](https://github.com/nf-core/tools) [`1.10.2`](https://github.com/nf-core/tools/releases/tag/1.10.2)
- [#262](https://github.com/nf-core/sarek/pull/262) - Update issue templates to fit the recommended community standards
- [#278](https://github.com/nf-core/sarek/pull/278), [#322](https://github.com/nf-core/sarek/pull/322) - Refactor docs
- [#284](https://github.com/nf-core/sarek/pull/284) - Update F1000Research publication to version 2
- [#284](https://github.com/nf-core/sarek/pull/284) - Update Scilifelab logo
- [#317](https://github.com/nf-core/sarek/pull/317) - Update `README.md` (Add: QBiC + Friederike/Gisela)
- [#320](https://github.com/nf-core/sarek/pull/278) - Set `MarkDuplicates MAX_RECORDS_IN_RAM` to default value

### Fixed

- [#229](https://github.com/nf-core/sarek/pull/229) - Fix `Control-FREEC` restart issue [#225](https://github.com/nf-core/sarek/issues/225)
- [#236](https://github.com/nf-core/sarek/pull/236) - Fix `GATK Mutect2` typo issue [#227](https://github.com/nf-core/sarek/issues/227)
- [#271](https://github.com/nf-core/sarek/pull/271) - Fix `ConcatVCF_Mutect2` `SIGPIPE` issue [#268](https://github.com/nf-core/sarek/issues/268)
- [#272](https://github.com/nf-core/sarek/pull/272) - Fix annotation `--tools merge` issue
- [#279](https://github.com/nf-core/sarek/pull/279) - Fix issue with `--step prepare_recalibration` [#267](https://github.com/nf-core/sarek/issues/267)
- [#280](https://github.com/nf-core/sarek/pull/280) - Use HTML codes instead of `<` and `>` in docs
- [#288](https://github.com/nf-core/sarek/pull/288) - Fix `test_annotation` profile
- [#289](https://github.com/nf-core/sarek/pull/289) - Random string added to `extractFastqFromDir` to avoid name collition
- [#290](https://github.com/nf-core/sarek/pull/290), [#323](https://github.com/nf-core/sarek/pull/323) - Faster solving of `Conda` environment
- [#293](https://github.com/nf-core/sarek/pull/293) - Fix typo issue when printing infos [#292](https://github.com/nf-core/sarek/issues/292)
- [#309](https://github.com/nf-core/sarek/pull/309) - Fixed concatenation of many VCF files
- [#310](https://github.com/nf-core/sarek/pull/310) - Fix Github Actions not running after November 16, 2020 (deprecated Github Actions API [#739](https://github.com/nf-core/tools/issues/739)
- [#329](https://github.com/nf-core/sarek/pull/329) - Simplify `Control-FREEC` usage
- [#331](https://github.com/nf-core/sarek/pull/331) - Replace `spread` operator by `combine` to remove `Nextflow` deprecation warning

### Removed

- [#234](https://github.com/nf-core/sarek/pull/243) - Removing obsolete script [#92](https://github.com/nf-core/sarek/issues/92)
- [#262](https://github.com/nf-core/sarek/pull/262) - Removing deprecated params: `annotateTools`, `annotateVCF`, `cadd_InDels`, `cadd_InDels_tbi`, `cadd_WG_SNVs`, `cadd_WG_SNVs_tbi`, `maxMultiqcEmailFileSize`, `noGVCF`, `noReports`, `noStrelkaBP`, `nucleotidesPerSecond`, `publishDirMode`, `sample`, `sampleDir`, `saveGenomeIndex`, `skipQC`, `snpEff_cache`, `targetBed`
- [#262](https://github.com/nf-core/sarek/pull/262) - Removing warning message about deprecated and obsolete params
- [#324](https://github.com/nf-core/sarek/pull/324) - `--no_gatk_spark` is now removed, use `--use_gatk_spark` instead
- [#324](https://github.com/nf-core/sarek/pull/324) - `--no_gvcf` is now removed, use `--generate_gvcf` instead

## [2.6.1](https://github.com/nf-core/sarek/releases/tag/2.6.1) - Gådokgaskatjåhkkå

Gådokgaskatjåhkkå is the highest peak in the Piellorieppe massif.

### Changed

- [#208](https://github.com/nf-core/sarek/pull/208) - Merge changes from the release PR
- [#208](https://github.com/nf-core/sarek/pull/208) - Bump version to `3.0dev`
- [#214](https://github.com/nf-core/sarek/pull/214) - Update `GATK` from `4.1.6.0` to `4.1.7.0`
- [#219](https://github.com/nf-core/sarek/pull/219) - Added `awsfulltest.yml` GitHub Actions workflow
- [#222](https://github.com/nf-core/sarek/pull/222) - Bump version to `2.6.1` and minor release
- [#223](https://github.com/nf-core/sarek/pull/223) - Apply comments from the release PR

### Fixed

- [#211](https://github.com/nf-core/sarek/pull/211) - Extend timeout for pushing to DockerHub for VEP containers
- [#212](https://github.com/nf-core/sarek/pull/212) - No AWS test on forks
- [#214](https://github.com/nf-core/sarek/pull/214) - Fix channels collision between `Freebayes` and `GATK Mutect2` [#200](https://github.com/nf-core/sarek/issues/200)
- [#214](https://github.com/nf-core/sarek/pull/214) - Fix warning Invalid tag value for `CreateIntervalBeds` [#209](https://github.com/nf-core/sarek/issues/209)
- [#214](https://github.com/nf-core/sarek/pull/214) - Fix `GATK Mutect2` issue [#210](https://github.com/nf-core/sarek/issues/210)
- [#219](https://github.com/nf-core/sarek/pull/219) - Updated `awstest.yml` GitHub actions workflow
- [#221](https://github.com/nf-core/sarek/pull/221) - Fix issue with `tmp_dir` in `BaseRecalibrator` process

## [2.6](https://github.com/nf-core/sarek/releases/tag/2.6) - Piellorieppe

Piellorieppe is one of the main massif in the Sarek National Park.

### Added

- [#76](https://github.com/nf-core/sarek/pull/76) - Add `GATK Spark` possibilities to Sarek
- [#87](https://github.com/nf-core/sarek/pull/87) - Add `GATK BaseRecalibrator` plot to `MultiQC` report
- [#115](https://github.com/nf-core/sarek/pull/115) - Add [@szilvajuhos](https://github.com/szilvajuhos) abstract for ESHG2020
- [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
- [#141](https://github.com/nf-core/sarek/pull/141) - Add containers for `WBcel235`
- [#150](https://github.com/nf-core/sarek/pull/150), [#151](https://github.com/nf-core/sarek/pull/151), [#154](https://github.com/nf-core/sarek/pull/154) - Add AWS mega test GitHub Actions
- [#153](https://github.com/nf-core/sarek/pull/153) - Add `CNVkit` possibilities to Sarek
- [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` version `3.3.0`
- [#163](https://github.com/nf-core/sarek/pull/163) - Add [MSIsensor](https://github.com/ding-lab/msisensor) in tools and container
- [#164](https://github.com/nf-core/sarek/pull/164) - Add `--no_gatk_spark` params and tests
- [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation
- [#169](https://github.com/nf-core/sarek/pull/169) - Add `RELEASE_CHECKLIST.md` document
- [#174](https://github.com/nf-core/sarek/pull/174) - Add `variant_calling.md` documentation
- [#175](https://github.com/nf-core/sarek/pull/175) - Add `Sentieon` documentation
- [#176](https://github.com/nf-core/sarek/pull/176) - Add empty `custom` genome in `genomes.config` to allow genomes that are not in `AWS iGenomes`
- [#179](https://github.com/nf-core/sarek/pull/179), [#201](https://github.com/nf-core/sarek/pull/201) - Add `FreeBayes` germline variant calling
- [#180](https://github.com/nf-core/sarek/pull/180) - Now saving Mapped BAMs (and creating TSV) in minimal setting
- [#182](https://github.com/nf-core/sarek/pull/182) - Add possibility to run `HaplotypeCaller` without `dbsnp` so it can be used to actually generate vcfs to build a set of known sites (cf [gatkforums](https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x))
- [#195](https://github.com/nf-core/sarek/pull/195) - Now creating TSV for duplicates marked BAMs in minimal setting
- [#195](https://github.com/nf-core/sarek/pull/195), [#202](https://github.com/nf-core/sarek/pull/202) - Add `--save_bam_mapped` params to save mapped BAMs
- [#197](https://github.com/nf-core/sarek/pull/197) - Add step `prepare_recalibration` to allow restart from DuplicatesMarked BAMs
- [#204](https://github.com/nf-core/sarek/pull/204) - Add step `Control-FREEC` to allow restart from pileup files
- [#205](https://github.com/nf-core/sarek/pull/205) - Add `--skip_markduplicates` to allow skipping the `MarkDuplicates` process

### Changed

- [#76](https://github.com/nf-core/sarek/pull/76) - Use `MarkDuplicatesSpark` instead of `MarkDuplicates`
- [#76](https://github.com/nf-core/sarek/pull/76) - Use `gatk4-spark` instead of `gatk4` in `environment.yml`
- [#80](https://github.com/nf-core/sarek/pull/80) - Re-bump `dev` branch
- [#85](https://github.com/nf-core/sarek/pull/85) - Use new merged vcf files for known indels to simplify setting up channel
- [#104](https://github.com/nf-core/sarek/pull/104) - Update Figure 1
- [#107](https://github.com/nf-core/sarek/pull/107) - Switch params to snake_case
- [#109](https://github.com/nf-core/sarek/pull/109) - Update publication with F1000Research preprint
- [#113](https://github.com/nf-core/sarek/pull/113) - Move social preview image
- [#120](https://github.com/nf-core/sarek/pull/120) - Sync TEMPLATE
- [#121](https://github.com/nf-core/sarek/pull/121) - Update `MultiQC` to `1.8`
- [#126](https://github.com/nf-core/sarek/pull/126), [#131](https://github.com/nf-core/sarek/pull/131) - Update docs
- [#131](https://github.com/nf-core/sarek/pull/131) - Use `nfcore/base:1.9` as base for containers
- [#131](https://github.com/nf-core/sarek/pull/131) - Update `Control-FREEC` to `11.5`
- [#131](https://github.com/nf-core/sarek/pull/131) - Update `FastQC` to `0.11.9`
- [#131](https://github.com/nf-core/sarek/pull/131) - Update `FreeBayes` to `1.3.2`
- [#131](https://github.com/nf-core/sarek/pull/131) - Update `Manta` to `1.6.0`
- [#131](https://github.com/nf-core/sarek/pull/131) - Update `Qualimap` to `2.2.2d`
- [#131](https://github.com/nf-core/sarek/pull/131) - Update `VEP` to `99.2`
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version from `75` to `87` for `GRCh37`
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version from `86` to `92` for `GRCh38`
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38`
- [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158), [#164](https://github.com/nf-core/sarek/pull/164), [#174](https://github.com/nf-core/sarek/pull/174), [#194](https://github.com/nf-core/sarek/pull/194), [#198](https://github.com/nf-core/sarek/pull/198), [#204](https://github.com/nf-core/sarek/pull/204) - Update docs
- [#164](https://github.com/nf-core/sarek/pull/164) - Update `gatk4-spark` from `4.1.4.1` to `4.1.6.0`
- [#180](https://github.com/nf-core/sarek/pull/180), [#195](https://github.com/nf-core/sarek/pull/195) - Improve minimal setting
- [#183](https://github.com/nf-core/sarek/pull/183), [#204](https://github.com/nf-core/sarek/pull/204) - Update `input.md` documentation
- [#197](https://github.com/nf-core/sarek/pull/197) - Output directory `DuplicateMarked` is now replaced by `DuplicatesMarked`
- [#204](https://github.com/nf-core/sarek/pull/204) - Output directory `controlFREEC` is now replaced by `Control-FREEC`

### Fixed

- [#83](https://github.com/nf-core/sarek/pull/83) - Fix some typos in `docs/input.md`
- [#107](https://github.com/nf-core/sarek/pull/107) - Fix linting
- [#110](https://github.com/nf-core/sarek/pull/110) - Fix `snpEff` report issue cf [#106](https://github.com/nf-core/sarek/issues/106)
- [#126](https://github.com/nf-core/sarek/pull/126) - Fix `iGenomes` paths
- [#127](https://github.com/nf-core/sarek/pull/127), [#128](https://github.com/nf-core/sarek/pull/128) - Fix `ASCAT`
- [#129](https://github.com/nf-core/sarek/pull/129) - Fix issue with Channel `channel ch_software_versions_yaml`
- [#129](https://github.com/nf-core/sarek/pull/129) - Apply @drpatelh fix for `mardown_to_html.py` compatibility with Python 2
- [#129](https://github.com/nf-core/sarek/pull/129) - Removed `Python` `3.7.3` from conda environment due to incompatibility
- [#129](https://github.com/nf-core/sarek/pull/129) - Change ascii characters that were not supported from the `output.md` docs
- [#140](https://github.com/nf-core/sarek/pull/140) - Fix extra T/N combinations for `ASCAT` cf [#136](https://github.com/nf-core/sarek/issues/136)
- [#141](https://github.com/nf-core/sarek/pull/141) - Fix `download_cache.nf` script to download cache for `snpEff` and `VEP`
- [#143](https://github.com/nf-core/sarek/pull/143) - Fix annotation CI testing with `snpEff` and `VEP`
- [#144](https://github.com/nf-core/sarek/pull/144) - Fix CircleCI for building `VEP` containers
- [#146](https://github.com/nf-core/sarek/pull/146) - Fix `--no_intervals` for `GATK Mutect2` cf [#135](https://github.com/nf-core/sarek/issues/135)
- [#156](https://github.com/nf-core/sarek/pull/156) - Fix typos
- [#156](https://github.com/nf-core/sarek/pull/156) - Fix issues with `dbsnp` files while using only `Sention` tools
- [#158](https://github.com/nf-core/sarek/pull/158) - Fix typo with `params.snpeff_cache` to decide containers for `snpEff`
- [#164](https://github.com/nf-core/sarek/pull/164) - Fix issues when running with `Sentieon`
- [#164](https://github.com/nf-core/sarek/pull/164) - Add more VCFs to annotation
- [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation to fix [#166](https://github.com/nf-core/sarek/issues/166)
- [#178](https://github.com/nf-core/sarek/pull/178) - Fix `Sentieon` variant calling, now using deduped bam files
- [#188](https://github.com/nf-core/sarek/pull/188) - Fix input/output channels for process `IndexBamFile` to match actual files in the `mapped.tsv` files
- [#189](https://github.com/nf-core/sarek/pull/189) - Fix `no_intervals` for process `HaplotypeCaller` (the file just need to actually exists...)
- [#197](https://github.com/nf-core/sarek/pull/197) - Fix issue with `--step recalibrate`
- [#197](https://github.com/nf-core/sarek/pull/197) - Fix typo in output directory `DuplicateMarked` -> `DuplicatesMarked`

### Deprecated

- [#107](https://github.com/nf-core/sarek/pull/107) - `--annotateTools` is now deprecated, use `--annotate_tools` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_InDels` is now deprecated, use `--cadd_indels` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_InDels_tbi` is now deprecated, use `--cadd_indels_tbi` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_WG_SNVs` is now deprecated, use `--cadd_wg_snvs` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_WG_SNVs_tbi` is now deprecated, use `--cadd_wg_snvs_tbi` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--maxMultiqcEmailFileSize` is now deprecated, use `--max_multiqc_email_size` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--noGVCF` is now deprecated, use `--no_gvcf` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--noStrelkaBP` is now deprecated, use `--no_strelka_bp` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--nucleotidesPerSecond` is now deprecated, use `--nucleotides_per_second` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--publishDirMode` is now deprecated, use `--publish_dir_mode` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--saveGenomeIndex` is now deprecated, use `--save_reference` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--skipQC` is now deprecated, use `--skip_qc` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--snpEff_cache` is now deprecated, use `--snpeff_cache` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--targetBed` is now deprecated, use `--target_bed` instead

### Removed

- [#107](https://github.com/nf-core/sarek/pull/107) - `--acLociGC` is now removed, use `--ac_loci_gc` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--acLoci` is now removed, use `--ac_loci` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--bwaIndex` is now removed, use `--bwa` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--chrDir` is now removed, use `--chr_dir` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--chrLength` is now removed, use `--chr_length` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--dbsnpIndex` is now removed, use `--dbsnp_index` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--fastaFai` is now removed, use `--fasta_fai` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--genomeDict` is now removed, use `--dict` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--genomeFile` is now removed, use `--fasta` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--genomeIndex` is now removed, use `--fasta_fai` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--germlineResourceIndex` is now removed, use `--germline_resource_index` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--germlineResource` is now removed, use `--germline_resource` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--igenomesIgnore` is now removed, use `--igenomes_ignore` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--knownIndelsIndex` is now removed, use `--known_indels_index` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--knownIndels` is now removed, use `--known_indels` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--singleCPUMem` is now removed, use `--single_cpu_mem` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--snpeffDb` is now removed, use `--snpeff_db` instead
- [#107](https://github.com/nf-core/sarek/pull/107) - `--vepCacheVersion` is now removed, use `--vep_cache_version` instead
- [#152](https://github.com/nf-core/sarek/pull/152) - Removed `Jenkinsfile`
- [#169](https://github.com/nf-core/sarek/pull/169) - Removed omicX from README
- [#181](https://github.com/nf-core/sarek/pull/181) - Remove duplicate code in `nextflow.config`

## [2.5.2](https://github.com/nf-core/sarek/releases/tag/2.5.2) - Jåkkåtjkaskajekna

Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.

### Added

- [#45](https://github.com/nf-core/sarek/pull/45) - Include Workflow figure in `README.md`
- [#46](https://github.com/nf-core/sarek/pull/46) - Add location to abstracts
- [#52](https://github.com/nf-core/sarek/pull/52) - Add support for mouse data `GRCm38`
- [#60](https://github.com/nf-core/sarek/pull/60) - Add `no_intervals` params
- [#60](https://github.com/nf-core/sarek/pull/60) - Add automatic generation of `intervals` file with `BuildIntervals` process
- [#60](https://github.com/nf-core/sarek/pull/60) - Add minimal support for minimal genome (only `fasta`, or `fasta` + `knownIndels`)
- [#60](https://github.com/nf-core/sarek/pull/60) - Add new processes (`IndexBamFile`, `IndexBamRecal`) to deal with optional usage of interval files and minimal genome
- [#60](https://github.com/nf-core/sarek/pull/60) - Add tests for minimal genome usage
- [#60](https://github.com/nf-core/sarek/pull/60) - Add new minimal genomes (`TAIR10`, `EB2`, `UMD3.1`, `bosTau8`, `WBcel235`, `ce10`, `CanFam3.1`, `canFam3`, `GRCz10`, `danRer10`, `BDGP6`, `dm6`, `EquCab2`, `equCab2`, `EB1`, `Galgal4`, `galGal4`, `Gm01`, `hg38`, `hg19`, `Mmul_1`, `mm10`, `IRGSP-1.0`, `CHIMP2.1.4`, `panTro4`, `Rnor_6.0`, `rn6`, `R64-1-1`, `sacCer3`, `EF2`, `Sbi1`, `Sscrofa10.2`, `susScr3`, `AGPv3`) to `igenomes.config`
- [#61](https://github.com/nf-core/sarek/pull/61) - Add params `split_fastq`
- [#61](https://github.com/nf-core/sarek/pull/61) - Add test `SPLITFASTQ`
- [#66](https://github.com/nf-core/sarek/pull/66) - Add `Sentieon` possibilities to Sarek

### Changed

- [#54](https://github.com/nf-core/sarek/pull/54) - Bump version to `2.5.2dev`
- [#60](https://github.com/nf-core/sarek/pull/60) - Some process (`BaseRecalibrator`, `ApplyBQSR`, `Mpileup`) have now optional usage of interval files
- [#60](https://github.com/nf-core/sarek/pull/60) - Update documentation
- [#71](https://github.com/nf-core/sarek/pull/71) - Update `README`
- [#71](https://github.com/nf-core/sarek/pull/71) - Update `CHANGELOG`
- [#74](https://github.com/nf-core/sarek/pull/74) - Update docs
- [#74](https://github.com/nf-core/sarek/pull/74) - Improve CI tests (both Jenkins and GitHub actions tests)
- [#74](https://github.com/nf-core/sarek/pull/74) - Move all CI from `ci-extra.yml` to `ci.yml`

### Removed

- [#46](https://github.com/nf-core/sarek/pull/46) - Remove mention of old `build.nf` script which was included in `main.nf`
- [#74](https://github.com/nf-core/sarek/pull/74) - Remove `download_image.sh` and `run_tests.sh` scripts
- [#76](https://github.com/nf-core/sarek/pull/76) - Remove `runOptions = "-u \$(id -u):\$(id -g)"` in `nextflow.config` to enable `Spark` possibilities

### Fixed

- [#40](https://github.com/nf-core/sarek/pull/40) - Fix issue with `publishDirMode` within `test` profile
- [#42](https://github.com/nf-core/sarek/pull/42) - Fix typos, and minor updates in `README.md`
- [#43](https://github.com/nf-core/sarek/pull/43) - Fix automated `VEP` builds with circleCI
- [#54](https://github.com/nf-core/sarek/pull/54) - Apply fixes from release `2.5.1`
- [#58](https://github.com/nf-core/sarek/pull/58) - Fix issue with `.interval_list` file from the `GATK` bundle [#56](https://github.com/nf-core/sarek/issues/56) that was not recognized in the `CreateIntervalsBed` process
- [#71](https://github.com/nf-core/sarek/pull/71) - Fix typos in `CHANGELOG`
- [#73](https://github.com/nf-core/sarek/pull/73) - Fix issue with label `memory_max` for `BaseRecalibrator` process [#72](https://github.com/nf-core/sarek/issues/72)

## [2.5.1](https://github.com/nf-core/sarek/releases/tag/2.5.1) - Årjep-Ålkatjjekna

Årjep-Ålkatjjekna is one of the two glaciers of the Ålkatj Massif.

### Added

- [#53](https://github.com/nf-core/sarek/pull/53) - Release `2.5.1`

### Fixed

- [#48](https://github.com/nf-core/sarek/issues/48) - Fix `singularity.autoMounts` issue
- [#49](https://github.com/nf-core/sarek/issues/49) - Use correct tag for annotation containers
- [#50](https://github.com/nf-core/sarek/issues/50) - Fix paths for scripts

## [2.5](https://github.com/nf-core/sarek/releases/tag/2.5) - Ålkatj

Ålkatj is one of the main massif in the Sarek National Park.

Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) template.

### Added

- [#2](https://github.com/nf-core/sarek/pull/2) - Create `nf-core/sarek` `environment.yml` file
- [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#7](https://github.com/nf-core/sarek/pull/7), [#9](https://github.com/nf-core/sarek/pull/9), [#10](https://github.com/nf-core/sarek/pull/10), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12) - Add CI for `nf-core/sarek`
- [#3](https://github.com/nf-core/sarek/pull/3) - Add preprocessing to `nf-core/sarek`
- [#4](https://github.com/nf-core/sarek/pull/4) - Add variant calling to `nf-core/sarek` with `HaplotypeCaller`, and single mode `Manta` and `Strelka`
- [#5](https://github.com/nf-core/sarek/pull/5), [#34](https://github.com/nf-core/sarek/pull/34) - Add variant calling to `nf-core/sarek` with `Manta`, `Strelka`, `Strelka Best Practices`, `GATK Mutect2`, `FreeBayes`, `ASCAT`, `ControlFREEC`
- [#6](https://github.com/nf-core/sarek/pull/6) - Add default containers for annotation to `nf-core/sarek`
- [#7](https://github.com/nf-core/sarek/pull/7) - Add `MultiQC`
- [#7](https://github.com/nf-core/sarek/pull/7) - Add annotation
- [#7](https://github.com/nf-core/sarek/pull/7) - Add social preview image in `png` and `svg` format
- [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#11](https://github.com/nf-core/sarek/pull/11), [#21](https://github.com/nf-core/sarek/pull/21) - Add helper script `run_tests.sh` to run different tests
- [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9) - Add automatic build of specific containers for annotation for `GRCh37`, `GRCh38` and `GRCm38` using `CircleCI`
- [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11) - Add helper script `build_reference.sh` to build small reference from [nf-core/test-datasets:sarek](https://github.com/nf-core/test-datasets/tree/sarek)
- [#7](https://github.com/nf-core/sarek/pull/7), [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12) - Add helper script `download_image.sh` to download containers for testing
- [#8](https://github.com/nf-core/sarek/pull/8) - Add test configuration for easier testing
- [#9](https://github.com/nf-core/sarek/pull/9), [#11](https://github.com/nf-core/sarek/pull/11) - Add scripts for `ASCAT`
- [#10](https://github.com/nf-core/sarek/pull/10) - Add `TIDDIT` to detect structural variants
- [#11](https://github.com/nf-core/sarek/pull/11) - Add automatic build of specific containers for annotation for `CanFam3.1` using `CircleCI`
- [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12) - Add posters and abstracts
- [#12](https://github.com/nf-core/sarek/pull/12) - Add helper script `make_snapshot.sh` to make an archive for usage on a secure cluster
- [#12](https://github.com/nf-core/sarek/pull/12) - Add helper scripts `filter_locifile.py` and `selectROI.py`
- [#12](https://github.com/nf-core/sarek/pull/12) - Use `label` for processes configuration
- [#13](https://github.com/nf-core/sarek/pull/13) - Add Citation documentation
- [#13](https://github.com/nf-core/sarek/pull/13) - Add `BamQC` process
- [#13](https://github.com/nf-core/sarek/pull/13) - Add `CompressVCFsnpEff` and `CompressVCFvep` processes
- [#18](https://github.com/nf-core/sarek/pull/18) - Add `--no-reports` option for tests + add snpEff,VEP,merge to MULTIPLE test
- [#18](https://github.com/nf-core/sarek/pull/18) - Add logo to `MultiQC` report
- [#18](https://github.com/nf-core/sarek/pull/18), [#29](https://github.com/nf-core/sarek/pull/29) - Add params `--skipQC` to skip specified QC tools
- [#18](https://github.com/nf-core/sarek/pull/18) - Add possibility to download other genome for `sareksnpeff` and `sarekvep` containers
- [#20](https://github.com/nf-core/sarek/pull/20) - Add `markdownlint` config file
- [#21](https://github.com/nf-core/sarek/pull/21) - Add tests for latest `Nextflow` version as well
- [#21](https://github.com/nf-core/sarek/pull/21) - Add `genomes.config` for genomes without `AWS iGenomes`
- [#24](https://github.com/nf-core/sarek/pull/24) - Added `GATK4 Mutect2` calling and filtering
- [#27](https://github.com/nf-core/sarek/pull/27), [#30](https://github.com/nf-core/sarek/pull/30) - Use Github actions for CI, linting and branch protection
- [#31](https://github.com/nf-core/sarek/pull/31) - Add `nf-core lint`
- [#31](https://github.com/nf-core/sarek/pull/31) - Add extra CI to `GitHub Actions` nf-core extra CI
- [#35](https://github.com/nf-core/sarek/pull/35) - Building indexes from [nf-core/test-datasets:sarek](https://github.com/nf-core/test-datasets/tree/sarek) for CI and small tests

### Changed

- [#1](https://github.com/nf-core/sarek/pull/1), [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#6](https://github.com/nf-core/sarek/pull/6), [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9), [#10](https://github.com/nf-core/sarek/pull/10), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12), [#18](https://github.com/nf-core/sarek/pull/18), [#20](https://github.com/nf-core/sarek/pull/20), [#21](https://github.com/nf-core/sarek/pull/21), [#23](https://github.com/nf-core/sarek/pull/23), [#29](https://github.com/nf-core/sarek/pull/29) - Update docs
- [#4](https://github.com/nf-core/sarek/pull/4) - Update `cancerit-allelecount` from `2.1.2` to `4.0.2`
- [#4](https://github.com/nf-core/sarek/pull/4) - Update `gatk4` from `4.1.1.0` to `4.1.2.0`
- [#7](https://github.com/nf-core/sarek/pull/7), [#23](https://github.com/nf-core/sarek/pull/23) - `--sampleDir` is now deprecated, use `--input` instead
- [#7](https://github.com/nf-core/sarek/pull/8), [#23](https://github.com/nf-core/sarek/pull/23) - `--annotateVCF` is now deprecated, use `--input` instead
- [#8](https://github.com/nf-core/sarek/pull/8), [#12](https://github.com/nf-core/sarek/pull/12) - Improve helper script `build.nf` for downloading and building reference files
- [#9](https://github.com/nf-core/sarek/pull/9) - `ApplyBQSR` is now parallelized
- [#9](https://github.com/nf-core/sarek/pull/9) - Fastq files are named following "${idRun}\_R1.fastq.gz" in the `FastQC` output for easier reporting
- [#9](https://github.com/nf-core/sarek/pull/9) - Status is now a map with `idpatient`, `idsample` as keys (ie: `status = statusMap[idPatient, idSample]`)
- [#9](https://github.com/nf-core/sarek/pull/9) - Use `ensembl-vep` `95.2` instead of `96.0`
- [#11](https://github.com/nf-core/sarek/pull/11) - Summary HTML from `VEP` is now in the `Reports` directory
- [#12](https://github.com/nf-core/sarek/pull/12) - Update configuration files
- [#12](https://github.com/nf-core/sarek/pull/12) - Disable `Docker` in `singularity` profile
- [#12](https://github.com/nf-core/sarek/pull/12) - Disable `Singularity` in `docker` profile
- [#12](https://github.com/nf-core/sarek/pull/12) - Disable `Docker` and `Singularity` in `conda` profile
- [#12](https://github.com/nf-core/sarek/pull/12) - Simplify `check_max()` function
- [#13](https://github.com/nf-core/sarek/pull/13) - Merge `BamQCmapped` and `BamQCrecalibrated` processes into `BamQC` process
- [#13](https://github.com/nf-core/sarek/pull/13) - Split `CompressVCF` process into `CompressVCFsnpEff` and `CompressVCFvep` processes
- [#16](https://github.com/nf-core/sarek/pull/16) - Make scripts in `bin/` and `scripts/` executable
- [#18](https://github.com/nf-core/sarek/pull/18) - Use `--no-reports` for TravisCI testing
- [#18](https://github.com/nf-core/sarek/pull/18) - Add `--no-reports` for all tests but MULTIPLE in Jenkins
- [#18](https://github.com/nf-core/sarek/pull/18), [#29](https://github.com/nf-core/sarek/pull/29) - `--noReports` is now `--skipQC all`
- [#18](https://github.com/nf-core/sarek/pull/18), [#21](https://github.com/nf-core/sarek/pull/21) - Update logo
- [#21](https://github.com/nf-core/sarek/pull/21) - Moved `smallGRCh37` path to `genomes.config`
- [#23](https://github.com/nf-core/sarek/pull/23) - Rename `genomeFile`, `genomeIndex` and `genomeDict` by `fasta`, `fastaFai` and `dict`
- [#23](https://github.com/nf-core/sarek/pull/23) - `--sample` is now deprecated, use `--input` instead
- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeFile` is now deprecated, use `--fasta` instead
- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeIndex` is now deprecated, use `--fastaFai` instead
- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeDict` is now deprecated, use `--dict` instead
- [#24](https://github.com/nf-core/sarek/pull/24) - `AWS iGenomes` config now contains germline resource for `GATK4 Mutect2`
- [#30](https://github.com/nf-core/sarek/pull/30) - Simplify code for `MapReads` process
- [#24](https://github.com/nf-core/sarek/pull/24) - `AWS iGenomes` config now contains germline resource for `GATK4 Mutect2`
- [#31](https://github.com/nf-core/sarek/pull/31) - Move extra CI to `GitHub Actions` nf-core extra CI
- [#32](https://github.com/nf-core/sarek/pull/32), [#33](https://github.com/nf-core/sarek/pull/33) - Install `ASCAT` with `conda` in the `environment.yml` file
- [#33](https://github.com/nf-core/sarek/pull/33) - Use `workflow.manifest.version` to specify workflow version in path to scripts for `ControlFREEC` and `VEP` processes
- [#35](https://github.com/nf-core/sarek/pull/35) - Building indexes is now done in `main.nf`
- [#35](https://github.com/nf-core/sarek/pull/35) - `build.nf` script now only download cache, so renamed to `downloadcache.nf`
- [#35](https://github.com/nf-core/sarek/pull/35) - Use `tabix` instead of `IGVtools` to build vcf indexes
- [#35](https://github.com/nf-core/sarek/pull/35) - Refactor references handling
- [#35](https://github.com/nf-core/sarek/pull/35) - Use Channel values instead of `referenceMap`
- [#37](https://github.com/nf-core/sarek/pull/37) - Bump version for Release
- [#38](https://github.com/nf-core/sarek/pull/38) - File names before merge is based on `${idSample}_${idRun}` instead of `${idRun}`

### Removed

- [#9](https://github.com/nf-core/sarek/pull/9) - Removed `relatedness2` graph from `vcftools stats`
- [#13](https://github.com/nf-core/sarek/pull/13) - Removed `BamQCmapped` and `BamQCrecalibrated` processes
- [#13](https://github.com/nf-core/sarek/pull/13) - Removed `CompressVCF`
- [#18](https://github.com/nf-core/sarek/pull/18) - Removed params `--noReports`
- [#24](https://github.com/nf-core/sarek/pull/18) - Removed `GATK3.X Mutect2`
- [#31](https://github.com/nf-core/sarek/pull/31) - Remove extra CI from `Travis CI` and `GitHub Actions` nf-core CI
- [#32](https://github.com/nf-core/sarek/pull/32), [#35](https://github.com/nf-core/sarek/pull/35) - Clean up `environment.yml` file
- [#35](https://github.com/nf-core/sarek/pull/35) - Remove building indexes from `build.nf` script
- [#35](https://github.com/nf-core/sarek/pull/35) - Remove helper script `build_reference.sh`
- [#35](https://github.com/nf-core/sarek/pull/35) - Remove `IGVtools`
- [#35](https://github.com/nf-core/sarek/pull/35) - Remove `GATK Mutect2` from `MULTIPLE` test
- [#35](https://github.com/nf-core/sarek/pull/35) - Remove `referenceMap` and `defineReferenceMap()` and use Channel values instead

### Fixed

- [#3](https://github.com/nf-core/sarek/pull/3) - Fix `Docker` ownership
- [#11](https://github.com/nf-core/sarek/pull/11) - Fix `MergeMpileup` PublishDir
- [#13](https://github.com/nf-core/sarek/pull/13) - Fix merge in annotation
- [#14](https://github.com/nf-core/sarek/pull/14) - Fix output name for vcf files
- [#16](https://github.com/nf-core/sarek/pull/16) - Fix path to `Rscript`
- [#18](https://github.com/nf-core/sarek/pull/18) - Improve cpu usage
- [#18](https://github.com/nf-core/sarek/pull/18) - Use same font for `nf-core` and `sarek` in ascii art
- [#20](https://github.com/nf-core/sarek/pull/20) - Use new logo in README
- [#20](https://github.com/nf-core/sarek/pull/20) - Fix path to references genomes
- [#22](https://github.com/nf-core/sarek/pull/22) - Fix `--singleCPUMem` issue
- [#30](https://github.com/nf-core/sarek/pull/30) - Fix choice between `inputPairReadsFastQC` and `inputBAMFastQC` channels
- [#31](https://github.com/nf-core/sarek/pull/31) - Fix badges according to nf-core lint
- [#31](https://github.com/nf-core/sarek/pull/31) - Fix `rcolorbrewer` version according to nf-core lint
- [#33](https://github.com/nf-core/sarek/pull/33) - Fix MD Linting
- [#38](https://github.com/nf-core/sarek/pull/38) - Avoid collision in `MultiQC`
- [#39](https://github.com/nf-core/sarek/pull/39) - Fix `ch_dbsnp` channel

### Deprecated

- [#23](https://github.com/nf-core/sarek/pull/23) - `--sample` is now deprecated, use `--input` instead
- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeFile` is now deprecated, use `--fasta` instead
- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeIndex` is now deprecated, use `--fastaFai` instead
- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeDict` is now deprecated, use `--dict` instead
- [#29](https://github.com/nf-core/sarek/pull/29) - `--noReports` is now deprecated, use `--skipQC all`

## [2.3.FIX1](https://github.com/SciLifeLab/Sarek/releases/tag/2.3.FIX1) - 2019-03-04

### Fixed

- [#742](https://github.com/SciLifeLab/Sarek/pull/742) - Fix output dirs (`HaplotypeCaller` that was not recognized by `annotate.nf` introduced by [#728](https://github.com/SciLifeLab/Sarek/pull/728))

## [2.3](https://github.com/SciLifeLab/Sarek/releases/tag/2.3) - Äpar - 2019-02-27

Äpar is one of the main massif in the Sarek National Park.

### Added

- [#628](https://github.com/SciLifeLab/Sarek/pull/628), [#722](https://github.com/SciLifeLab/Sarek/pull/722) - `ASCAT` now use `.gc` file
- [#712](https://github.com/SciLifeLab/Sarek/pull/712), [#718](https://github.com/SciLifeLab/Sarek/pull/718) - Added possibilities to run Sarek with `conda`
- [#719](https://github.com/SciLifeLab/Sarek/pull/719) - Annotation documentation
- [#719](https://github.com/SciLifeLab/Sarek/pull/719) - Helper script to download `snpeff` and `VEP` cache files
- [#719](https://github.com/SciLifeLab/Sarek/pull/719) - New `--annotation_cache`, `--snpEff_cache`, `--vep_cache` parameters
- [#719](https://github.com/SciLifeLab/Sarek/pull/719) - Possibility to use cache wen annotating with `snpEff` and `VEP`
- [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Add path to ASCAT `.gc` file in `igenomes.config`
- [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Update `Sarek-data` submodule with multiple patients TSV file
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Add `cadd_WG_SNVs`, `cadd_WG_SNVs_tbi`, `cadd_InDels`, `cadd_InDels_tbi` and `cadd_cache` params
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Add `tabix` indexed cache for `VEP`
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - New `DownloadCADD` process to download CADD files
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Specify values for `cadd_WG_SNVs`, `cadd_WG_SNVs_tbi`, `cadd_InDels`, `cadd_InDels_tbi` and `cadd_cache` params in `munin.conf` file
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Use `cadd_cache` param for optional use of CADD VEP plugin in `annotate.nf`
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - `VEP` cache has now fasta files for `--HGVS`
- [#735](https://github.com/SciLifeLab/Sarek/pull/735) - Added `--exome` for `Manta`, and for `StrelkaBP`
- [#735](https://github.com/SciLifeLab/Sarek/pull/735) - Added `Travis CI` test for targeted

### Changed

- [#710](https://github.com/SciLifeLab/Sarek/pull/710) - Improve release checklist and script
- [#711](https://github.com/SciLifeLab/Sarek/pull/711) - Improve configuration priorities
- [#716](https://github.com/SciLifeLab/Sarek/pull/716) - Update paths to containers and `AWS iGenomes`
- [#717](https://github.com/SciLifeLab/Sarek/pull/717) - `checkFileExtension` has changed to `hasExtension`, and now only verify if file has extension
- [#717](https://github.com/SciLifeLab/Sarek/pull/717) - `fastqFiles` renamed to `inputFiles`
- [#717](https://github.com/SciLifeLab/Sarek/pull/717) - `mapping` step can now map BAM files too
- [#717](https://github.com/SciLifeLab/Sarek/pull/717) - `MapReads` can now convert BAM to FASTQ and feed it to BWA on the fly
- [#717](https://github.com/SciLifeLab/Sarek/pull/717), [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Update documentation
- [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `snpeff` and `vep` containers are now built with `conda`
- [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `vepCacheVersion` is now defined in `conf/genomes.config` or `conf/igenomes.config`
- [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Add path to ASCAT `.gc` file in `igenomes.config`
- [#722](https://github.com/SciLifeLab/Sarek/pull/722) - Update `Sarek-data` submodule
- [#723](https://github.com/SciLifeLab/Sarek/pull/723), [#725](https://github.com/SciLifeLab/Sarek/pull/725) - Update docs
- [#724](https://github.com/SciLifeLab/Sarek/pull/724) - Improved `AWS batch` configuration
- [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Improved usage of `targetBED` params
- [#728](https://github.com/SciLifeLab/Sarek/pull/728) - `Strelka` Best Practices output is now prefixed with `StrelkaBP_`
- [#728](https://github.com/SciLifeLab/Sarek/pull/728) - VCFs and Annotated VCFs are now ordered by Patient, then tools
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Merge `buildContainers.nf` and `buildReferences.nf` in `build.nf`
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Reduce number of CPUs for `RunVEP` to `4` cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#faster)
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Update `VEP` from `95.1` to `95.2`

### Removed

- [#715](https://github.com/SciLifeLab/Sarek/pull/715) - Remove `defReferencesFiles` function from `buildReferences.nf`
- [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `snpEff` base container is no longer used
- [#721](https://github.com/SciLifeLab/Sarek/pull/721) - Remove `COSMIC` docs
- [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Remove `defineDirectoryMap()`
- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Remove `--database` option for VEP cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#faster)

### Fixed

- [#720](https://github.com/SciLifeLab/Sarek/pull/720) - `bamQC` is now run on the recalibrated BAMs, and not after `MarkDuplicates`
- [#726](https://github.com/SciLifeLab/Sarek/pull/726) - Fix `Ascat` ref file input (one file can't be a set)
- [#727](https://github.com/SciLifeLab/Sarek/pull/727) - `bamQC` outputs are no longer overwritten (name of dir is now the file instead of sample)
- [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Fix issue with annotation that was consuming `cache` channels
- [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Fix multi sample TSV file [#691](https://github.com/SciLifeLab/Sarek/issues/691)
- [#733](https://github.com/SciLifeLab/Sarek/pull/733) - Fix the possibility to specify reference files on the command line

## [2.2.2](https://github.com/SciLifeLab/Sarek/releases/tag/2.2.2) - 2018-12-19

### Added

- [#671](https://github.com/SciLifeLab/Sarek/pull/671) - New `publishDirMode` param and docs
- [#673](https://github.com/SciLifeLab/Sarek/pull/673), [#675](https://github.com/SciLifeLab/Sarek/pull/675), [#676](https://github.com/SciLifeLab/Sarek/pull/676) - Profiles for BinAC and CFC clusters in Tübingen
- [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Add container for `CreateIntervalBeds`
- [#692](https://github.com/SciLifeLab/Sarek/pull/692), [#697](https://github.com/SciLifeLab/Sarek/pull/697) - Add `AWS iGenomes` possibilities (within `conf/igenomes.conf`)
- [#694](https://github.com/SciLifeLab/Sarek/pull/694) - Add monochrome and grey logos for light or dark background
- [#698](https://github.com/SciLifeLab/Sarek/pull/698) - Add btb profile for munin server
- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Add `font-ttf-dejavu-sans-mono` `2.37` and `fontconfig` `2.1dev` to container

### Changed

- [#663](https://github.com/SciLifeLab/Sarek/pull/663) - Update `do_release.sh` script
- [#671](https://github.com/SciLifeLab/Sarek/pull/671) - `publishDir` modes are now params
- [#677](https://github.com/SciLifeLab/Sarek/pull/677), [#698](https://github.com/SciLifeLab/Sarek/pull/698), [#703](https://github.com/SciLifeLab/Sarek/pull/703) - Update docs
- [#678](https://github.com/SciLifeLab/Sarek/pull/678) - Changing `VEP` to `v92` and adjusting CPUs for `VEP`
- [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Update old `awsbatch` configuration
- [#682](https://github.com/SciLifeLab/Sarek/pull/682) - Specifications for memory and cpus for `awsbatch`
- [#693](https://github.com/SciLifeLab/Sarek/pull/693) - `Qualimap bamQC` is now ran after mapping and after recalibration for better QC
- [#700](https://github.com/SciLifeLab/Sarek/pull/700) - Update `GATK` to `4.0.9.0`
- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Update `FastQC` to `0.11.8`
- [#705](https://github.com/SciLifeLab/Sarek/pull/705) - Change `--TMP_DIR` by `--tmp-dir` for `GATK` `4.0.9.0` `BaseRecalibrator`
- [#706](https://github.com/SciLifeLab/Sarek/pull/706) - Update `Travis CI` testing

### Fixed

- [#665](https://github.com/SciLifeLab/Sarek/pull/665) - Input bam file now has always the same name (whether it is from a single fastq pair or multiple) in the `MarkDuplicates` process, so metrics too
- [#672](https://github.com/SciLifeLab/Sarek/pull/672) - Process `PullSingularityContainers` from `buildContainers.nf` now expect a file with the correct `.simg` extension for singularity images, and no longer the `.img` one
- [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Add `publishDirMode` for `germlineVC.nf`
- [#700](https://github.com/SciLifeLab/Sarek/pull/700) - Fix [#699](https://github.com/SciLifeLab/Sarek/issues/699) missing DP in the FORMAT column VCFs for Mutect2
- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Fix [#701](https://github.com/SciLifeLab/Sarek/issues/701)
- [#705](https://github.com/SciLifeLab/Sarek/pull/705) - Fix [#704](https://github.com/SciLifeLab/Sarek/issues/704)

## [2.2.1](https://github.com/SciLifeLab/Sarek/releases/tag/2.2.1) - 2018-10-04

### Changed

- [#646](https://github.com/SciLifeLab/Sarek/pull/646) - Update [`pathfindr`](https://github.com/NBISweden/pathfindr) submodule
- [#659](https://github.com/SciLifeLab/Sarek/pull/659) - Update `Nextflow` to `0.32.0`
- [#660](https://github.com/SciLifeLab/Sarek/pull/660) - Update docs

### Fixed

- [#657](https://github.com/SciLifeLab/Sarek/pull/657) - Fix `RunMultiQC.nf` bug
- [#659](https://github.com/SciLifeLab/Sarek/pull/659) - Fix bugs due to updating `Nextflow`

## [2.2.0](https://github.com/SciLifeLab/Sarek/releases/tag/2.2.0) - Skårki - 2018-09-21

Skårki is one of the main massif in the Sarek National Park.

### Added

- [#613](https://github.com/SciLifeLab/Sarek/pull/613) - Add Issue Templates (bug report and feature request)
- [#614](https://github.com/SciLifeLab/Sarek/pull/614) - Add PR Template
- [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Add presentation
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update documentation
- [#620](https://github.com/SciLifeLab/Sarek/pull/620) - Add `tmp/` to `.gitignore`
- [#625](https://github.com/SciLifeLab/Sarek/pull/625) - Add [`pathfindr`](https://github.com/NBISweden/pathfindr) as a submodule
- [#635](https://github.com/SciLifeLab/Sarek/pull/635) - To process targeted sequencing with a target BED
- [#639](https://github.com/SciLifeLab/Sarek/pull/639) - Add a complete example analysis to docs
- [#640](https://github.com/SciLifeLab/Sarek/pull/640), [#642](https://github.com/SciLifeLab/Sarek/pull/642) - Add helper script for changing version number

### Changed

- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update `Nextflow` required version
- [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Use `splitCsv` instead of `readlines`
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update `CHANGELOG`
- [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Improve install script
- [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Simplify tests
- [#627](https://github.com/SciLifeLab/Sarek/pull/627), [#629](https://github.com/SciLifeLab/Sarek/pull/629), [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Refactor docs
- [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Refactor config
- [#632](https://github.com/SciLifeLab/Sarek/pull/632) - Use 2 threads and 2 cpus `FastQC` processes
- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Update tool version gathering
- [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Use correct `.simg` extension for Singularity images
- [#639](https://github.com/SciLifeLab/Sarek/pull/639) - Smaller refactoring of the docs
- [#640](https://github.com/SciLifeLab/Sarek/pull/640) - Update RELEASE_CHECKLIST
- [#642](https://github.com/SciLifeLab/Sarek/pull/642) - `MultiQC` 1.5 -> 1.6
- [#642](https://github.com/SciLifeLab/Sarek/pull/642) - `Qualimap` 2.2.2a -> 2.2.2b
- [#642](https://github.com/SciLifeLab/Sarek/pull/642) - Update `conda` channel order priorities
- [#642](https://github.com/SciLifeLab/Sarek/pull/642) - `VCFanno` 0.2.8 -> 0.3.0
- [#642](https://github.com/SciLifeLab/Sarek/pull/642) - `VCFtools` 0.1.15 -> 0.1.16

### Removed

- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Remove old Issue Template
- [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Remove old Dockerfiles
- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Remove old comments

### Fixed

- [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Fix `VEP` tests
- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Fix links in MD files

## [2.1.0](https://github.com/SciLifeLab/Sarek/releases/tag/2.1.0) - Ruotes - 2018-08-14

Ruotes is one of the main massif in the Sarek National Park.

### Added

- [#555](https://github.com/SciLifeLab/Sarek/pull/555) - `snpEff` output into `VEP`
- [#556](https://github.com/SciLifeLab/Sarek/pull/556) - `Strelka` Best Practices
- [#563](https://github.com/SciLifeLab/Sarek/pull/563) - Use `SnpEFF` reports in `MultiQC`
- [#568](https://github.com/SciLifeLab/Sarek/pull/568) - `VCFTools` process `RunVcftools` for QC
- [#574](https://github.com/SciLifeLab/Sarek/pull/574), [#580](https://github.com/SciLifeLab/Sarek/pull/580) - Abstracts for `NPMI`, `JOBIM` and `EACR25`
- [#577](https://github.com/SciLifeLab/Sarek/pull/577) - New repository for testing: [Sarek-data](https://github.com/SciLifeLab/Sarek-data)
- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New library `QC` for functions `bamQC`, `bcftools`, `samtoolsStats`, `vcftools`, `getVersionBCFtools`, `getVersionGATK`, `getVersionManta`, `getVersionSnpEFF`, `getVersionStrelka`, `getVersionVCFtools`, `getVersionVEP`
- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New Processes `GetVersionBCFtools`, `GetVersionGATK`, `GetVersionManta`, `GetVersionSnpEFF`, `GetVersionStrelka`, `GetVersionVCFtools`, `GetVersionVEP`
- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New `Python` script `bin/scrape_tool_versions.py` inspired by @ewels and @apeltzer
- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New QC Process `RunVcftools`
- [#596](https://github.com/SciLifeLab/Sarek/pull/596) - New profile for `BinAC` cluster
- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - New function `sarek_ascii()` in `SarekUtils`
- [#599](https://github.com/SciLifeLab/Sarek/pull/599), [#602](https://github.com/SciLifeLab/Sarek/pull/602) - New Process `CompressVCF`
- [#601](https://github.com/SciLifeLab/Sarek/pull/601), [#603](https://github.com/SciLifeLab/Sarek/pull/603) - Container for `GATK4`
- [#606](https://github.com/SciLifeLab/Sarek/pull/606) - Add test data as a submodule from [`Sarek-data`](https://github.com/SciLifeLab/Sarek-data)
- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Add documentation on how to install Nextflow on `bianca`

### Changed

- [#557](https://github.com/SciLifeLab/Sarek/pull/557), [#583](https://github.com/SciLifeLab/Sarek/pull/583), [#585](https://github.com/SciLifeLab/Sarek/pull/585), [#588](https://github.com/SciLifeLab/Sarek/pull/588) - Update help
- [#560](https://github.com/SciLifeLab/Sarek/pull/560) - `GitHub` langage for the repository is now `Nextflow`
- [#561](https://github.com/SciLifeLab/Sarek/pull/561) - `do_all.sh` build only containers for one genome reference (default `GRCh38`) only
- [#571](https://github.com/SciLifeLab/Sarek/pull/571) - Only one container for all QC tools
- [#582](https://github.com/SciLifeLab/Sarek/pull/582), [#587](https://github.com/SciLifeLab/Sarek/pull/587) - Update figures
- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - Function `defineDirectoryMap()` is now part of `SarekUtils`
- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - Process `GenerateMultiQCconfig` replace by function `createMultiQCconfig()`
- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - `extractBams()` now takes an extra parameter
- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Move `checkFileExtension()`, `checkParameterExistence()`, `checkParameterList()`, `checkReferenceMap()`, `checkRefExistence()`, `extractBams()`, `extractGenders()`, `returnFile()`, `returnStatus()` and `returnTSV()` functions to `SarekUtils`
- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Reduce data footprint for Process `CreateRecalibrationTable`
- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Replace deprecated operator `phase` by `join`
- [#599](https://github.com/SciLifeLab/Sarek/pull/599) - Merge is tested with `ANNOTATEALL`
- [#604](https://github.com/SciLifeLab/Sarek/pull/604) - Synching `GRCh38` `wgs_calling_regions` bedfiles
- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - One container approach
- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Update to `GATK4`
- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update `Nextflow` required version
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update `CHANGELOG`
- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated `Nextflow` `$name` syntax with `withName`

### Fixed

- [#560](https://github.com/SciLifeLab/Sarek/pull/560) - Display message for `repository` and `containerPath`
- [#566](https://github.com/SciLifeLab/Sarek/pull/566) - `slurmDownload` profile
- [#579](https://github.com/SciLifeLab/Sarek/pull/579), [#584](https://github.com/SciLifeLab/Sarek/pull/584) - `Manta` output reorganized after modification for `Strelka Best Practices` process
- [#585](https://github.com/SciLifeLab/Sarek/pull/583) - Trace file is plain txt
- [#590](https://github.com/SciLifeLab/Sarek/pull/590), [#593](https://github.com/SciLifeLab/Sarek/pull/593) - Fix `Singularity` installation in `Travis CI` testing
- [#598](https://github.com/SciLifeLab/Sarek/pull/598), [#601](https://github.com/SciLifeLab/Sarek/pull/601) - Fixes for `Python` script `selectROI.py` to work with `CLC` viewer

### Removed

- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Remove `Mutect1`

## [2.0.0](https://github.com/SciLifeLab/Sarek/releases/tag/2.0.0) - 2018-03-23

First release under the `Sarek` name, from the National Park in Northern Sweden.

### Added

- Basic wrapper script
- Abstract, posters and figures
- ROI selector and `FreeBayes` sanitizer scripts
- New logo and icon for the project
- Check for existing tumor/normal channel
- `SarekUtils` with `checkParams()`, `checkParameterList()`, `checkParameterExistence()` and `isAllowedParams()` functions
- Some `runOptions` for `docker` (prevent some user right problem)
- This `CHANGELOG`

### Changed

- `CAW` is now `Sarek`
- Dissect Workflow in 5 new scripts: `annotate.nf`, `main.nf`, `germlineVC.nf`, `runMultiQC.nf` and `somaticVC.nf`
- `report.html`, `timeline.html` and `trace.html` are generated in `Reports/`
- `--version` is now used to define the workflow version
- Most params are now defined in the `base.config` file instead of in the scripts
- Update `RELEASE_CHECKLIST.md`
- `checkParams()`, `checkParameterList()`, `checkParameterExistence()` and `isAllowedParams()` in script functions are now called within `SarekUtils`
- `nf_required_version` is now `params.nfRequiredVersion`
- In `buildReferences.nf` script, channels now begin by `ch_`, and files by `f_`
- Use `PublishDir mode: 'link'` instead of `copy`
- `directoryMap` now contains `params.outDir`
- [#539](https://github.com/SciLifeLab/Sarek/issues/539) - Use Nextflow support of scratch
- Reordered `Travis CI` tests
- Update documentation
- `MultiQC` version in container from v`1.4` to v`1.5`
- `vepgrch37` container base image from `release_90.6` to `release_92`
- `vepgrch38` container base image from `release_90.6` to `release_92`
- `VEP` version in containers from v`90` to v`91`
- `nucleotidesPerSecond` is now `params.nucleotidesPerSecond`
- Default `params.tag` is now `latest` instead of current version, so `--tag` needs to be specified with the right version to be sure of using the `containers` corresponding

### Deprecated

- `standard` profile
- `uppmax-localhost.config` file

### Removed

- `scripts/skeleton_batch.sh`
- Old data and tsv files
- `UPPMAX` directories from containers
- `--step` in `annotate.nf`, `germlineVC.nf` and `somatic.nf`
- Some `runOptions` for `Singularity` (binding not needed anymore on `UPPMAX`)
- `download` profile

### Fixed

- [#530](https://github.com/SciLifeLab/Sarek/issues/530) - Use `$PWD` for default `outDir`
- [#533](https://github.com/SciLifeLab/Sarek/issues/533) - Replace `VEP` `--pick` option by `--per_gene`

## [1.2.5](https://github.com/SciLifeLab/Sarek/releases/tag/1.2.5) - 2018-01-18

### Added

- `Zenodo` for DOI
- Delivery README
- Document use of the `--sampleDir` option
- Contributing Guidelines
- Issue Templates
- Release Checklist
- `--outDir`
- `awsbatch` profile
- `aws-batch.config` config file
- `--noBAMQC` params (failing sometimes on `Bianca`)

### Changed

- Update `Nextflow` to `0.26.0` (new fancy report + `AWS Batch`)
- Extra time on `Travis CI` testing
- Replace `bundleDir` by `params.genome_base`
- Update `MultiQC` to `1.3` (`MEGAQC` FTW)
- Move and rename some test files

### Fixed

- Version of `COSMIC` `GRCh37` `v83`
- Write an error message when `--sampleDir` does not find any FASTQ files
- `base.config` for `ConcatVCF` process
- File specification for `recalibrationReport` in `RecalibrateBam` process (got error on `AWS Batch`)

## [1.2.4](https://github.com/SciLifeLab/Sarek/releases/tag/1.2.4) - 2017-10-27

### Fixed

- [#488](https://github.com/SciLifeLab/Sarek/issues/488) - Better CPU requirements for `ConcatVCF`
- [#489](https://github.com/SciLifeLab/Sarek/issues/489) - Exception handling for `ASCAT`
- [#490](https://github.com/SciLifeLab/Sarek/issues/490) - CPU requirements for `runSingleStrelka` and `runSingleManta`

## [1.2.3](https://github.com/SciLifeLab/Sarek/releases/tag/1.2.3) - 2017-10-18

### Fixed

- [#357](https://github.com/SciLifeLab/Sarek/issues/357) - `ASCAT` works for `GRCh38`
- [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on `/scratch`
- [#475](https://github.com/SciLifeLab/Sarek/issues/475) - 16 cpus for local executor
- [#480](https://github.com/SciLifeLab/Sarek/issues/480) - No `tsv` file needed for step `annotate`

## [1.2.2](https://github.com/SciLifeLab/Sarek/releases/tag/1.2.2) - 2017-10-06

### Fixed

- [#479](https://github.com/SciLifeLab/Sarek/issues/479) - Typo in `uppmax-localhost.config`

## [1.2.1](https://github.com/SciLifeLab/Sarek/releases/tag/1.2.1) - 2017-10-06

### Changed

- `runascat` and `runconvertallelecounts` containers are now replaced by `r-base`
- `willmclaren/ensembl-vep:release_90.5` is now base for `vepgrch37` and `vepgrch38`

### Removed

- `vep` container
- `strelka_config.ini` file

### Fixed

- [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on /scratch
- [#472](https://github.com/SciLifeLab/Sarek/issues/472) - Update function to check `Nextflow` version
- [#473](https://github.com/SciLifeLab/Sarek/issues/473) - Remove `returnMin()` function

## [1.2.0](https://github.com/SciLifeLab/Sarek/releases/tag/1.2.0) - 2017-10-02

### Changed

- Fix version for Manuscript

## [1.1](https://github.com/SciLifeLab/Sarek/releases/tag/1.1) - 2017-09-15

### Added

- `Singularity` possibilities

### Changed

- Reports made by default
- Intervals file can be a bed file
- Normal sample preprocessing + `HaplotypeCaller` is possible
- Better `Travis CI` tests

### Fixed

- Memory requirements

## [1.0](https://github.com/SciLifeLab/Sarek/releases/tag/1.0) - 2017-02-16

### Added

- `Docker` possibilities

## [0.9](https://github.com/SciLifeLab/Sarek/releases/tag/0.9) - 2016-11-16

## [0.8](https://github.com/SciLifeLab/Sarek/releases/tag/0.8) - 2016-11-16

## [0.1] - 2016-04-05