diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md index e50bec2d4d..fd15eb72a5 100644 --- a/.github/RELEASE_CHECKLIST.md +++ b/.github/RELEASE_CHECKLIST.md @@ -12,6 +12,8 @@ 4. Sync `dev` and checkout a new branch for the release 5. Bump version: - `nf-core bump-version . ` + - edit `docs/images/sarek_indices_subway.svg` + - generate a new `docs/images/sarek_indices_subway.png` - edit `docs/images/sarek_subway.svg` - generate a new `docs/images/sarek_subway.png` - edit `docs/images/sarek_workflow.svg` @@ -28,6 +30,8 @@ - `git checkout upstream/master -- CHANGELOG.md` 14. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version 15. Checkout figures from `master` + - `git checkout upstream/master -- docs/images/sarek_indices_subway.svg` + - `git checkout upstream/master -- docs/images/sarek_indices_subway.png` - `git checkout upstream/master -- docs/images/sarek_subway.svg` - `git checkout upstream/master -- docs/images/sarek_subway.png` - `git checkout upstream/master -- docs/images/sarek_workflow.svg` diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ecd51ab94..54bdb8c847 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,29 @@ 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). +## [3.1.1](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. diff --git a/conf/igenomes.config b/conf/igenomes.config index 578798c523..9d85de95fb 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -138,6 +138,13 @@ params { bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" + snpeff_db = 'UMD3.1.75' + snpeff_genome = 'UMD3.1' + snpeff_version = '5.1' + vep_cache_version = 94 + vep_genome = 'UMD3.1' + vep_species = 'bos_taurus' + vep_version = '106.1' } 'WBcel235' { bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" @@ -214,6 +221,13 @@ params { 'R64-1-1' { bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" + snpeff_db = 'R64-1-1.105' + snpeff_genome = 'R64-1-1' + snpeff_version = '5.1' + vep_cache_version = 106 + vep_genome = 'R64-1-1' + vep_species = 'saccharomyces_cerevisiae' + vep_version = '106.1' } 'EF2' { bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" diff --git a/conf/modules/markduplicates.config b/conf/modules/markduplicates.config index 08bfd85688..9979ae8152 100644 --- a/conf/modules/markduplicates.config +++ b/conf/modules/markduplicates.config @@ -57,7 +57,7 @@ process { } withName: 'GATK4_MARKDUPLICATES' { - ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true' + ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT' ext.prefix = { "${meta.id}.md.cram" } ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) } publishDir = [ diff --git a/docs/images/sarek_indices_subway.png b/docs/images/sarek_indices_subway.png index 04672354e8..42a01b0458 100644 Binary files a/docs/images/sarek_indices_subway.png and b/docs/images/sarek_indices_subway.png differ diff --git a/docs/images/sarek_indices_subway.svg b/docs/images/sarek_indices_subway.svg index 7190bdb088..380cba4b39 100644 --- a/docs/images/sarek_indices_subway.svg +++ b/docs/images/sarek_indices_subway.svg @@ -7,9 +7,9 @@ viewBox="0 0 744.09448 524.40944" id="svg4924" version="1.1" - inkscape:version="1.1 (c4e8f9e, 2021-05-24)" + inkscape:version="1.2.1 (1:1.2.1+202210291243+9c6d41e410)" sodipodi:docname="sarek_indices_subway.svg" - inkscape:export-filename="/Users/monarchy/Projects/Coding/sarek/docs/images/sarek_indices_subway.png" + inkscape:export-filename="sarek_indices_subway.png" inkscape:export-xdpi="90" inkscape:export-ydpi="90" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" @@ -2963,9 +2963,9 @@ borderopacity="1.0" inkscape:pageopacity="1" inkscape:pageshadow="2" - inkscape:zoom="0.8521196" - inkscape:cx="407.21983" - inkscape:cy="359.69129" + inkscape:zoom="3.4084784" + inkscape:cx="148.01326" + inkscape:cy="148.45334" inkscape:document-units="px" inkscape:current-layer="g2380" showgrid="false" @@ -2975,13 +2975,15 @@ fit-margin-bottom="0" units="mm" width="200mm" - inkscape:window-width="1305" - inkscape:window-height="847" + inkscape:window-width="2560" + inkscape:window-height="1412" inkscape:window-x="0" - inkscape:window-y="25" - inkscape:window-maximized="0" + inkscape:window-y="0" + inkscape:window-maximized="1" showguides="false" - inkscape:pagecheckerboard="0" /> + inkscape:pagecheckerboard="0" + inkscape:showpageshadow="2" + inkscape:deskcolor="#d1d1d1" /> @@ -3006,7 +3008,7 @@ 3.1.0 + id="flowPara2359-7">3.1.1 3.1.0 + id="flowPara2359-7">3.1.1 3.1.0 + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:18.0525px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro Bold';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal">3.1.1 diff --git a/modules.json b/modules.json index cce1c81995..001413f95f 100644 --- a/modules.json +++ b/modules.json @@ -197,7 +197,8 @@ }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67" + "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67", + "patch": "modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff" }, "gatk4/markduplicatesspark": { "branch": "master", diff --git a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff new file mode 100644 index 0000000000..8ba713052b --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff @@ -0,0 +1,45 @@ +Changes in module 'nf-core/gatk4/markduplicates' +--- modules/nf-core/gatk4/markduplicates/main.nf ++++ modules/nf-core/gatk4/markduplicates/main.nf +@@ -2,10 +2,10 @@ + tag "$meta.id" + label 'process_medium' + +- conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) ++ conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0 bioconda::samtools=1.16.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': +- 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" ++ 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0': ++ 'quay.io/biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0' }" + + input: + tuple val(meta), path(bam) +@@ -38,20 +38,20 @@ + """ + gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\ + $input_list \\ +- --OUTPUT ${prefix} \\ ++ --OUTPUT ${prefix}.bam \\ + --METRICS_FILE ${prefix}.metrics \\ + --TMP_DIR . \\ + ${reference} \\ + $args + +- +- if [[ ${prefix} == *.cram ]]; then +- mv ${prefix}.bai ${prefix}.crai +- fi ++ samtools view -Ch -T ${fasta} -o ${prefix} ${prefix}.bam ++ rm ${prefix}.bam ++ samtools index ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') ++ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +-} ++} +************************************************************ diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 02f78bda2d..10ca04f100 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.3.0.0 bioconda::samtools=1.16.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0': + 'quay.io/biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:551156018e5580fb94d44632dfafbc9c27005a0e-0' }" input: tuple val(meta), path(bam) @@ -38,20 +38,20 @@ process GATK4_MARKDUPLICATES { """ gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\ $input_list \\ - --OUTPUT ${prefix} \\ + --OUTPUT ${prefix}.bam \\ --METRICS_FILE ${prefix}.metrics \\ --TMP_DIR . \\ ${reference} \\ $args - - if [[ ${prefix} == *.cram ]]; then - mv ${prefix}.bai ${prefix}.crai - fi + samtools view -Ch -T ${fasta} -o ${prefix} ${prefix}.bam + rm ${prefix}.bam + samtools index ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 30dad82366..a11a1a4dcd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -280,7 +280,7 @@ manifest { description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing' mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' - version = '3.1' + version = '3.1.1' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 64c319f511..1e75f7fa45 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -278,7 +278,6 @@ }, "cf_chrom_len": { "type": "string", - "default": "None", "fa_icon": "fas fa-ruler-horizontal", "description": "Specify a custom chromosome length file.", "help_text": "Control-FREEC requires a file containing all chromosome lenghts. By default the fasta.fai is used. If the fasta.fai file contains chromosomes not present in the intervals, it fails (see: https://github.com/BoevaLab/FREEC/issues/106).\n\nIn this case, a custom chromosome length can be specified. It must be of the same format as the fai, but only contain the relevant chromosomes.\n\n\n\n",