diff --git a/CHANGELOG.md b/CHANGELOG.md index df995e232a..1b69aa18ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,7 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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) - Improve variant calling subworkflows +- [#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` @@ -54,7 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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` - [#563](https://github.com/nf-core/sarek/pull/563) - Updated subway map -- [#571](https://github.com/nf-core/sarek/pull/571) - Including and using GATK4's mergeVcfs. Removing the local module `concat_vcf`. +- [#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 - [#578](https://github.com/nf-core/sarek/pull/578) - Updated module deeptools/bamcoverage @@ -94,6 +94,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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 +- [#571](https://github.com/nf-core/sarek/pull/571) - Removed the local module `concat_vcf`. ## [2.7.1](https://github.com/nf-core/sarek/releases/tag/2.7.1) - Pårtejekna diff --git a/subworkflows/local/annotate.nf b/subworkflows/local/annotate.nf index a9c386b011..50a1476e47 100644 --- a/subworkflows/local/annotate.nf +++ b/subworkflows/local/annotate.nf @@ -8,15 +8,15 @@ include { ANNOTATION_ENSEMBLVEP } from '../nf-core/annotatio workflow ANNOTATE { take: - vcf // channel: [ val(meta), vcf ] - tools - snpeff_db - snpeff_cache - vep_genome - vep_species - vep_cache_version - vep_cache - vep_extra_files + vcf // channel: [ val(meta), vcf ] + tools // Mandatory, list of tools to apply + snpeff_db + snpeff_cache + vep_genome + vep_species + vep_cache_version + vep_cache + vep_extra_files main: ch_reports = Channel.empty() diff --git a/subworkflows/local/germline_variant_calling.nf b/subworkflows/local/germline_variant_calling.nf index 13757a2b24..a5bf1f56f4 100644 --- a/subworkflows/local/germline_variant_calling.nf +++ b/subworkflows/local/germline_variant_calling.nf @@ -7,21 +7,22 @@ include { RUN_FREEBAYES } from '../nf-core/variantcalling/freebayes/main.n include { RUN_HAPLOTYPECALLER } from '../nf-core/variantcalling/haplotypecaller/main.nf' include { RUN_MANTA_GERMLINE } from '../nf-core/variantcalling/manta/germline/main.nf' include { RUN_STRELKA_SINGLE } from '../nf-core/variantcalling/strelka/single/main.nf' -include { RUN_CNVKIT_GERMLINE } from '../nf-core/variantcalling/cnvkit/germline/main.nf' +include { RUN_CNVKIT_GERMLINE } from '../nf-core/variantcalling/cnvkit/germline/main.nf' //include { TIDDIT } from './variantcalling/tiddit.nf' workflow GERMLINE_VARIANT_CALLING { take: - cram_recalibrated // channel: [mandatory] cram - dbsnp // channel: [mandatory] dbsnp - dbsnp_tbi // channel: [mandatory] dbsnp_tbi - dict // channel: [mandatory] dict - fasta // channel: [mandatory] fasta - fasta_fai // channel: [mandatory] fasta_fai - intervals // channel: [mandatory] intervals/target regions - intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed - intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped - // joint_germline // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment + tools // Mandatory, list of tools to apply + cram_recalibrated // channel: [mandatory] cram + dbsnp // channel: [mandatory] dbsnp + dbsnp_tbi // channel: [mandatory] dbsnp_tbi + dict // channel: [mandatory] dict + fasta // channel: [mandatory] fasta + fasta_fai // channel: [mandatory] fasta_fai + intervals // channel: [mandatory] intervals/target regions + intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed + intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped + // joint_germline // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment main: @@ -60,7 +61,7 @@ workflow GERMLINE_VARIANT_CALLING { // CNVKIT - if(params.tools.contains('cnvkit')){ + if(tools.contains('cnvkit')){ cram_recalibrated_cnvkit_germline = cram_recalibrated .map{ meta, cram, crai -> [meta, [], cram] @@ -75,7 +76,7 @@ workflow GERMLINE_VARIANT_CALLING { } // DEEPVARIANT - if(params.tools.contains('deepvariant')){ + if(tools.contains('deepvariant')){ RUN_DEEPVARIANT(cram_recalibrated_intervals, dict, fasta, fasta_fai) deepvariant_vcf = Channel.empty().mix(RUN_DEEPVARIANT.out.deepvariant_vcf,RUN_DEEPVARIANT.out.deepvariant_gvcf) @@ -83,7 +84,7 @@ workflow GERMLINE_VARIANT_CALLING { } // FREEBAYES - if (params.tools.contains('freebayes')){ + if (tools.contains('freebayes')){ // Remap channel for Freebayes cram_recalibrated_intervals_freebayes = cram_recalibrated_intervals .map{ meta, cram, crai, intervals -> @@ -96,7 +97,7 @@ workflow GERMLINE_VARIANT_CALLING { } // HAPLOTYPECALLER - if (params.tools.contains('haplotypecaller')){ + if (tools.contains('haplotypecaller')){ RUN_HAPLOTYPECALLER(cram_recalibrated_intervals, fasta, fasta_fai, @@ -110,7 +111,7 @@ workflow GERMLINE_VARIANT_CALLING { } // MANTA - if (params.tools.contains('manta')){ + if (tools.contains('manta')){ RUN_MANTA_GERMLINE (cram_recalibrated_intervals_gz_tbi, dict, fasta, @@ -121,7 +122,7 @@ workflow GERMLINE_VARIANT_CALLING { } // STRELKA - if (params.tools.contains('strelka')){ + if (tools.contains('strelka')){ RUN_STRELKA_SINGLE(cram_recalibrated_intervals_gz_tbi, dict, fasta, diff --git a/subworkflows/local/pair_variant_calling.nf b/subworkflows/local/pair_variant_calling.nf index 53b6b415bb..e5bcca5cb0 100644 --- a/subworkflows/local/pair_variant_calling.nf +++ b/subworkflows/local/pair_variant_calling.nf @@ -11,7 +11,7 @@ include { RUN_CNVKIT_SOMATIC } from '../nf-core/variantca workflow PAIR_VARIANT_CALLING { take: - tools + tools // Mandatory, list of tools to apply cram_pair // channel: [mandatory] cram dbsnp // channel: [mandatory] dbsnp dbsnp_tbi // channel: [mandatory] dbsnp_tbi diff --git a/subworkflows/local/tumor_variant_calling.nf b/subworkflows/local/tumor_variant_calling.nf index 04854fb656..2ef58e26e3 100644 --- a/subworkflows/local/tumor_variant_calling.nf +++ b/subworkflows/local/tumor_variant_calling.nf @@ -12,20 +12,20 @@ include { RUN_CNVKIT_TUMORONLY } from '../nf-core/variantcall workflow TUMOR_ONLY_VARIANT_CALLING { take: - tools // Mandatory, list of tools to apply - cram_recalibrated // channel: [mandatory] cram - dbsnp // channel: [mandatory] dbsnp - dbsnp_tbi // channel: [mandatory] dbsnp_tbi - dict // channel: [mandatory] dict - fasta // channel: [mandatory] fasta - fasta_fai // channel: [mandatory] fasta_fai - intervals // channel: [mandatory] intervals/target regions - intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed + tools // Mandatory, list of tools to apply + cram_recalibrated // channel: [mandatory] cram + dbsnp // channel: [mandatory] dbsnp + dbsnp_tbi // channel: [mandatory] dbsnp_tbi + dict // channel: [mandatory] dict + fasta // channel: [mandatory] fasta + fasta_fai // channel: [mandatory] fasta_fai + intervals // channel: [mandatory] intervals/target regions + intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped - germline_resource // channel: [optional] germline_resource - germline_resource_tbi // channel: [optional] germline_resource_tbi - panel_of_normals // channel: [optional] panel_of_normals - panel_of_normals_tbi // channel: [optional] panel_of_normals_tbi + germline_resource // channel: [optional] germline_resource + germline_resource_tbi // channel: [optional] germline_resource_tbi + panel_of_normals // channel: [optional] panel_of_normals + panel_of_normals_tbi // channel: [optional] panel_of_normals_tbi chr_files mappability diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 68cc8e1bef..d0d00fdab7 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -770,6 +770,7 @@ workflow SAREK { // GERMLINE VARIANT CALLING GERMLINE_VARIANT_CALLING( + params.tools, cram_variant_calling_status_normal, dbsnp, dbsnp_tbi,