diff --git a/CHANGELOG.md b/CHANGELOG.md index 106c24c75d..efcaeb52fd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -89,10 +89,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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` +- [#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 ### Fixed diff --git a/conf/modules.config b/conf/modules.config index 6facf23688..0689a032a3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1091,21 +1091,21 @@ process{ if (params.tools && params.tools.split(',').contains('tiddit')) { //TIDDIT - withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' { + withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' { ext.prefix = {"${meta.id}.tiddit.normal"} } - withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' { + withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' { ext.prefix = {"${meta.id}.tiddit.tumor"} } //SVDB - withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' { + withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:SVDB_MERGE' { ext.prefix = { "${meta.id}.tiddit" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" }, - pattern: "*vcf" + pattern: "*{vcf,vcf.gz}" ] } } diff --git a/subworkflows/local/pair_variant_calling.nf b/subworkflows/local/pair_variant_calling.nf index 4f315e0278..3656cc467e 100644 --- a/subworkflows/local/pair_variant_calling.nf +++ b/subworkflows/local/pair_variant_calling.nf @@ -11,9 +11,7 @@ include { RUN_CNVKIT } from '../nf-core/variantca include { RUN_MPILEUP as RUN_MPILEUP_NORMAL } from '../nf-core/variantcalling/mpileup/main' include { RUN_MPILEUP as RUN_MPILEUP_TUMOR } from '../nf-core/variantcalling/mpileup/main' include { RUN_ASCAT_SOMATIC } from '../nf-core/variantcalling/ascat/main' -include { RUN_TIDDIT as RUN_TIDDIT_NORMAL } from '../nf-core/variantcalling/tiddit/main.nf' -include { RUN_TIDDIT as RUN_TIDDIT_TUMOR } from '../nf-core/variantcalling/tiddit/main.nf' -include { SVDB_MERGE } from '../../modules/nf-core/modules/svdb/merge/main.nf' +include { RUN_TIDDIT_SOMATIC } from '../nf-core/variantcalling/tiddit/tiddit_somatic/main' workflow PAIR_VARIANT_CALLING { take: @@ -224,17 +222,9 @@ workflow PAIR_VARIANT_CALLING { [meta, tumor_cram, tumor_crai] } - RUN_TIDDIT_NORMAL(cram_normal, fasta, bwa) - RUN_TIDDIT_TUMOR(cram_tumor, fasta, bwa) - SVDB_MERGE(RUN_TIDDIT_NORMAL.out.tiddit_vcf.join(RUN_TIDDIT_TUMOR.out.tiddit_vcf) - .map{meta, vcf_normal, vcf_tumor -> - [meta, [vcf_normal, vcf_tumor]] - }, false) - tiddit_vcf = SVDB_MERGE.out.vcf - - ch_versions = ch_versions.mix(RUN_TIDDIT_NORMAL.out.versions) - ch_versions = ch_versions.mix(RUN_TIDDIT_TUMOR.out.versions) - ch_versions = ch_versions.mix(SVDB_MERGE.out.versions) + RUN_TIDDIT_SOMATIC(cram_normal, cram_tumor, fasta, bwa) + tiddit_vcf = RUN_TIDDIT_SOMATIC.out.tiddit_vcf + ch_versions = ch_versions.mix(RUN_TIDDIT_SOMATIC.out.versions) } emit: diff --git a/subworkflows/nf-core/variantcalling/tiddit/tiddit_somatic/main.nf b/subworkflows/nf-core/variantcalling/tiddit/tiddit_somatic/main.nf new file mode 100644 index 0000000000..3b9754fca2 --- /dev/null +++ b/subworkflows/nf-core/variantcalling/tiddit/tiddit_somatic/main.nf @@ -0,0 +1,32 @@ +include { RUN_TIDDIT as RUN_TIDDIT_NORMAL } from '../main.nf' +include { RUN_TIDDIT as RUN_TIDDIT_TUMOR } from '../main.nf' +include { SVDB_MERGE } from '../../../../../modules/nf-core/modules/svdb/merge/main.nf' + +workflow RUN_TIDDIT_SOMATIC { + take: + cram_normal + cram_tumor + fasta + bwa + + main: + + ch_versions = Channel.empty() + RUN_TIDDIT_NORMAL(cram_normal, fasta, bwa) + RUN_TIDDIT_TUMOR(cram_tumor, fasta, bwa) + RUN_TIDDIT_NORMAL.out.tiddit_vcf.dump(tag:"normal") + RUN_TIDDIT_TUMOR.out.tiddit_vcf.dump(tag:"tumor") + SVDB_MERGE(RUN_TIDDIT_NORMAL.out.tiddit_vcf.join(RUN_TIDDIT_TUMOR.out.tiddit_vcf) + .map{meta, vcf_normal, vcf_tumor -> + [meta, [vcf_normal, vcf_tumor]] + }, false) + tiddit_vcf = SVDB_MERGE.out.vcf + + ch_versions = ch_versions.mix(RUN_TIDDIT_NORMAL.out.versions) + ch_versions = ch_versions.mix(RUN_TIDDIT_TUMOR.out.versions) + ch_versions = ch_versions.mix(SVDB_MERGE.out.versions) + + emit: + versions = ch_versions + tiddit_vcf +}