diff --git a/CHANGELOG.md b/CHANGELOG.md index 143b186d66..bde5dea7c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### 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) ### Deprecated diff --git a/conf/modules.config b/conf/modules.config index 7500d8f199..529ae701a8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -607,6 +607,9 @@ process{ ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" } ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1' ext.when = { params.tools && params.tools.split(',').contains('freebayes') } + publishDir = [ + enabled: false + ] } withName: 'BCFTOOLS_SORT' { diff --git a/tests/test_tools.yml b/tests/test_tools.yml index f3b74b8f00..d90a0a9af3 100644 --- a/tests/test_tools.yml +++ b/tests/test_tools.yml @@ -31,6 +31,8 @@ - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn + - path: results/cnvkit + should_exist: false - name: Run variant calling on tumor_only sample with cnvkit command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools cnvkit tags: @@ -50,6 +52,8 @@ - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cnr - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cns - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.targetcoverage.cnn + - path: results/cnvkit + should_exist: false - name: Run variant calling on germline sample with cnvkit command: nextflow run main.nf -profile test,tools_germline,docker --tools cnvkit tags: @@ -70,6 +74,8 @@ - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cnr - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cns - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.targetcoverage.cnn + - path: results/cnvkit + should_exist: false - name: Run variant calling on somatic samples with controlfreec command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec tags: @@ -96,6 +102,8 @@ - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz + - path: results/cnvkit + should_exist: false - name: Run variant calling on somatic samples with controlfreec without intervals command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec --no_intervals -stub-run tags: @@ -126,6 +134,10 @@ - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_sample.cpn - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz + - path: results/controlfreec + should_exist: false + - path: results/mpileup + should_exist: false - name: Run variant calling on tumor_only sample with controlfreec command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools controlfreec -stub-run tags: @@ -150,6 +162,10 @@ - path: results/variant_calling/controlfreec/sample2/sample2_ratio.txt - path: results/variant_calling/controlfreec/sample2/sample2_sample.cpn - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz + - path: results/controlfreec + should_exist: false + - path: results/mpileup + should_exist: false - name: Run variant calling on germline sample with deepvariant command: nextflow run main.nf -profile test,tools_germline,docker --tools deepvariant tags: @@ -170,6 +186,8 @@ - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi + - path: results/deepvariant + should_exist: false - name: Run variant calling on germline sample with deepvariant without intervals command: nextflow run main.nf -profile test,tools_germline,docker --tools deepvariant --no_intervals tags: @@ -194,6 +212,8 @@ - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi + - path: results/deepvariant + should_exist: false - name: Run variant calling on germline sample with freebayes command: nextflow run main.nf -profile test,targeted,docker --tools freebayes tags: @@ -235,6 +255,8 @@ - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi + - path: results/freebayes + should_exist: false - name: Run variant calling on germline sample with freebayes without intervals command: nextflow run main.nf -profile test,docker --tools freebayes --no_intervals tags: @@ -276,6 +298,8 @@ - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi + - path: results/freebayes + should_exist: false - name: Run variant calling on somatic sample with freebayes command: nextflow run main.nf -profile test,pair,targeted,docker --tools freebayes tags: @@ -345,6 +369,8 @@ - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi + - path: results/freebayes + should_exist: false - name: Run variant calling on somatic sample with freebayes without intervals command: nextflow run main.nf -profile test,pair,targeted,docker --tools freebayes --no_intervals tags: @@ -406,6 +432,8 @@ - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi + - path: results/freebayes + should_exist: false # - name: Run variant calling on tumor_only sample with freebayes # command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools freebayes @@ -447,6 +475,8 @@ - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi + - path: results/haplotypecaller + should_exist: false - name: Run variant calling on germline sample with haplotypecaller without intervals command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals tags: @@ -470,7 +500,8 @@ - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi - + - path: results/haplotypecaller + should_exist: false - name: Run joint germline variant calling with haplotypecaller command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --joint_germline true --step variant_calling tags: @@ -488,7 +519,8 @@ - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi - + - path: results/haplotypecaller + should_exist: false - name: Run variant calling on germline sample with manta command: nextflow run main.nf -profile test,tools_germline,docker --tools manta tags: @@ -504,6 +536,8 @@ - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.qual - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi + - path: results/manta + should_exist: false - name: Run variant calling on germline sample with manta without intervals command: nextflow run main.nf -profile test,tools_germline,docker --tools manta --no_intervals tags: @@ -523,6 +557,8 @@ - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.qual - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi + - path: results/manta + should_exist: false - name: Run variant calling on tumor_only sample with manta command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta tags: @@ -538,6 +574,8 @@ - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.qual - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi + - path: results/manta + should_exist: false - name: Run variant calling on tumor_only sample with manta without intervals command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta --no_intervals tags: @@ -557,6 +595,8 @@ - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.qual - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi + - path: results/manta + should_exist: false - name: Run variant calling on somatic sample with manta command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta tags: @@ -584,6 +624,8 @@ - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi + - path: results/manta + should_exist: false - name: Run variant calling on somatic sample with manta without intervals command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta --no_intervals tags: @@ -615,6 +657,8 @@ - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi + - path: results/manta + should_exist: false - name: Run variant calling on tumor_only sample to test mpileup command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup tags: @@ -623,6 +667,8 @@ files: - path: results/multiqc - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz + - path: results/mpileup + should_exist: false - name: Run variant calling on tumor_only sample to test mpileup without intervals command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup --no_intervals tags: @@ -635,6 +681,8 @@ - path: results/no_intervals.bed.gz - path: results/no_intervals.bed.gz.tbi - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz + - path: results/mpileup + should_exist: false - name: Run variant calling on germline sample to test mpileup command: nextflow run main.nf -profile test,tools_germline,docker --tools mpileup tags: @@ -643,6 +691,8 @@ files: - path: results/multiqc - path: results/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz + - path: results/mpileup + should_exist: false - name: Run variant calling on germline sample to test mpileup without intervals command: nextflow run main.nf -profile test,tools_germline,docker --tools mpileup --no_intervals tags: @@ -655,6 +705,8 @@ - path: results/no_intervals.bed.gz - path: results/no_intervals.bed.gz.tbi - path: results/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz + - path: results/mpileup + should_exist: false - name: Run variant calling on tumor only sample with mutect2 command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mutect2 tags: @@ -678,6 +730,8 @@ - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi + - path: results/mutect2 + should_exist: false - name: Run variant calling on tumor only sample with mutect2 without intervals command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mutect2 --no_intervals tags: @@ -705,6 +759,8 @@ - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi + - path: results/mutect2 + should_exist: false - name: Run variant calling on somatic sample with msisensor-pro command: nextflow run main.nf -profile test,tools_somatic,docker --tools msisensorpro tags: @@ -717,6 +773,8 @@ - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_dis - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_germline - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_somatic + - path: results/msisensorpro + should_exist: false - name: Run variant calling on germline sample with strelka command: nextflow run main.nf -profile test,tools_germline,docker --tools strelka tags: @@ -734,6 +792,8 @@ - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi + - path: results/strelka + should_exist: false - name: Run variant calling on germline sample with strelka without intervals command: nextflow run main.nf -profile test,tools_germline,docker --tools strelka --no_intervals tags: @@ -755,6 +815,8 @@ - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi + - path: results/strelka + should_exist: false - name: Run variant calling on tumor only sample with strelka command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools strelka tags: @@ -772,6 +834,8 @@ - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi + - path: results/strelka + should_exist: false - name: Run variant calling on tumor only sample with strelka without intervals command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools strelka --no_intervals tags: @@ -793,6 +857,8 @@ - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi + - path: results/strelka + should_exist: false - name: Run variant calling on somatic sample with strelka command: nextflow run main.nf -profile test,tools_somatic,docker --tools strelka tags: @@ -822,6 +888,8 @@ - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi + - path: results/strelka + should_exist: false - name: Run variant calling on somatic sample with strelka without intervals command: nextflow run main.nf -profile test,tools_somatic,docker --tools strelka --no_intervals tags: @@ -855,6 +923,8 @@ - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi + - path: results/strelka + should_exist: false - name: Run variant calling on somatic sample with strelka & manta (StrelkaBP) command: nextflow run main.nf -profile test,tools_somatic,docker --tools strelka,manta tags: @@ -902,6 +972,10 @@ - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi + - path: results/manta + should_exist: false + - path: results/strelka + should_exist: false - name: Run variant calling on somatic sample with & manta (StrelkaBP) without intervals command: nextflow run main.nf -profile test,tools_somatic,docker --tools strelka,manta --no_intervals tags: @@ -953,6 +1027,10 @@ - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi + - path: results/manta + should_exist: false + - path: results/strelka + should_exist: false - name: Run variant calling on somatic sample with tiddit command: nextflow run main.nf -profile test,tools_somatic,docker --tools tiddit tags: @@ -979,6 +1057,8 @@ - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.vcf.gz + - path: results/tiddit + should_exist: false - name: Run variant calling on germline sample with tiddit command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit tags: @@ -995,6 +1075,8 @@ - path: results/variant_calling/tiddit/sample1/sample1.tiddit.ploidies.tab - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz.tbi + - path: results/tiddit + should_exist: false - name: Run variant calling on tumor_only sample with tiddit command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit tags: @@ -1011,3 +1093,5 @@ - path: results/variant_calling/tiddit/sample2/sample2.tiddit.ploidies.tab - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz.tbi + - path: results/tiddit + should_exist: false