From aebd413e27229d425b01f3e14273fef30cb85262 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Sun, 17 Jul 2022 14:10:13 +0200 Subject: [PATCH 1/2] merge tests/nextflow.config in conf/test.config --- conf/test.config | 34 ++++++++++++++++++++++++++++++++++ tests/nextflow.config | 34 ---------------------------------- tests/test_bam_remap.yml | 2 +- tests/test_only_paired_VC.yml | 2 +- tests/test_tools.yml | 26 +++++++++++++------------- 5 files changed, 49 insertions(+), 49 deletions(-) delete mode 100644 tests/nextflow.config diff --git a/conf/test.config b/conf/test.config index dda176d7e9..1b168196e0 100644 --- a/conf/test.config +++ b/conf/test.config @@ -195,3 +195,37 @@ profiles { params.input = "${projectDir}/tests/csv/3.0/bam_for_remapping.csv" } } + +process { + withName:'FREEC_SOMATIC'{ + ext.args = { + [ + "sample":[ + inputformat: 'pileup', + mateorientation: 'FR' + ], + "general" :[ + bedgraphoutput: "TRUE", + noisydata: "TRUE", + minexpectedgc: "0", + readcountthreshold: "1", + sex: meta.sex, + window: "10", + ], + "control":[ + inputformat: "pileup", + mateorientation: "FR" + ] + ] + } + } + + withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{ + //sample name from when the test data was generated + ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " } + } + + withName: 'FILTERVARIANTTRANCHES'{ + ext.args = { "--info-key CNN_1D --indel-tranche 0" } + } +} diff --git a/tests/nextflow.config b/tests/nextflow.config deleted file mode 100644 index 3c70399da2..0000000000 --- a/tests/nextflow.config +++ /dev/null @@ -1,34 +0,0 @@ -process { - - withName:'FREEC_SOMATIC'{ - ext.args = { [ - "sample":[ - inputformat: 'pileup', - mateorientation: 'FR' - ], - "general" :[ - bedgraphoutput: "TRUE", - noisydata: "TRUE", - minexpectedgc: "0", - readcountthreshold: "1", - sex: meta.sex, - window: "10", - ], - "control":[ - inputformat: "pileup", - mateorientation: "FR" - ] - ] - } - } - - withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{ - //sample name from when the test data was generated - ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " } - } - - withName: 'FILTERVARIANTTRANCHES'{ - ext.args = { "--info-key CNN_1D --indel-tranche 0" } - } - -} diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml index 840c67b6e0..9e91c19342 100644 --- a/tests/test_bam_remap.yml +++ b/tests/test_bam_remap.yml @@ -1,5 +1,5 @@ - name: Run alignment to fastq and then remap on bam files - command: nextflow run main.nf -profile test,alignment_to_fastq,docker -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,alignment_to_fastq,docker tags: - alignment_to_fastq diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml index 143c2731c7..58ca79ba1e 100644 --- a/tests/test_only_paired_VC.yml +++ b/tests/test_only_paired_VC.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal - command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit -c ./tests/nextflow.config --only_paired_variant_calling + command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit --only_paired_variant_calling tags: - cnvkit - somatic diff --git a/tests/test_tools.yml b/tests/test_tools.yml index 60ed11f5b9..1a5af70301 100644 --- a/tests/test_tools.yml +++ b/tests/test_tools.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic samples with cnvkit - command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_somatic,docker --tools cnvkit tags: - cnvkit - somatic @@ -32,7 +32,7 @@ - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.call.cns - name: Run variant calling on tumor_only sample with cnvkit - command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools cnvkit -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools cnvkit tags: - cnvkit - tumor_only @@ -51,7 +51,7 @@ - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.call.cns - name: Run variant calling on germline sample with cnvkit - command: nextflow run main.nf -profile test,tools_germline,docker --tools cnvkit -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_germline,docker --tools cnvkit tags: - cnvkit - germline @@ -71,7 +71,7 @@ - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.call.cns - name: Run variant calling on somatic samples with controlfreec - command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec tags: - controlfreec - somatic @@ -96,7 +96,7 @@ - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn - name: Run variant calling on somatic samples with controlfreec without intervals - command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec -c ./tests/nextflow.config --no_intervals -stub-run + command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec --no_intervals -stub-run tags: - controlfreec - no_intervals @@ -239,7 +239,7 @@ # - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi - name: Run variant calling on germline sample with haplotypecaller - command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller -c ./tests/nextflow.config --step variant_calling + command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling tags: - germline - haplotypecaller @@ -256,7 +256,7 @@ - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi - name: Run variant calling on germline sample with haplotypecaller without intervals - command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller -c ./tests/nextflow.config --step variant_calling --no_intervals + command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals tags: - germline - haplotypecaller @@ -274,7 +274,7 @@ - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi # - name: Run joint germline variant calling with haplotypecaller -# command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline -c ./tests/nextflow.config +# command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline # tags: # - germline # - gvcf @@ -288,7 +288,7 @@ # - path: results/csv/variantcalled.csv # - name: Run joint germline variant calling with haplotypecaller without intervals -# command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline --no_intervals -c ./tests/nextflow.config +# command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline --no_intervals # tags: # - germline # - gvcf @@ -448,7 +448,7 @@ - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with mutect2 - command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 tags: - mutect2_manual - manual @@ -617,7 +617,7 @@ - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with tiddit - command: nextflow run main.nf -profile test,tools_somatic,docker --tools tiddit -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_somatic,docker --tools tiddit tags: - tiddit - somatic @@ -634,7 +634,7 @@ - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.ploidies.tab - name: Run variant calling on germline sample with tiddit - command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit tags: - tiddit - germline @@ -645,7 +645,7 @@ - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz.tbi - name: Run variant calling on tumor_only sample with tiddit - command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit -c ./tests/nextflow.config + command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit tags: - tiddit - tumor_only From fcd2636ed02c131f2014ffd7269c42989d3a8381 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Sun, 17 Jul 2022 14:13:59 +0200 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ef0aafd225..8693ee185d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -89,6 +89,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#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 - [#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` ### Fixed