From acf90e2113dbb13e222927bbb2a527752838796e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 8 Sep 2023 10:58:20 +0200 Subject: [PATCH 1/3] better comment --- subworkflows/local/bam_variant_calling_tumor_only_all/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf index 45cca72c4a..ccdf370b61 100644 --- a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf +++ b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf @@ -1,5 +1,5 @@ // -// TUMOR VARIANT CALLING +// TUMOR ONLY VARIANT CALLING // Should be only run on patients without normal sample // From ffbf28a88071ca4c6e511744d04033b087b51779 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 8 Sep 2023 10:58:32 +0200 Subject: [PATCH 2/3] better test coverage --- tests/config/tags.yml | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/tests/config/tags.yml b/tests/config/tags.yml index c8e001a193..ed64360a2c 100644 --- a/tests/config/tags.yml +++ b/tests/config/tags.yml @@ -207,6 +207,9 @@ cnvkit: - modules/nf-core/cnvkit/batch/main.nf - modules/nf-core/cnvkit/reference/main.nf - subworkflows/local/bam_variant_calling_cnvkit/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - subworkflows/local/prepare_reference_cnvkit/main.nf - tests/test_cnvkit.yml @@ -222,7 +225,9 @@ controlfreec: - modules/nf-core/controlfreec/makegraph/main.nf - modules/nf-core/samtools/mpileup/main.nf - subworkflows/local/bam_variant_calling_mpileup/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf - subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf - tests/test_controlfreec.yml @@ -233,6 +238,7 @@ deepvariant: - modules/nf-core/gatk4/mergevcfs/main.nf - modules/nf-core/tabix/tabix/main.nf - subworkflows/local/bam_variant_calling_deepvariant/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - tests/test_deepvariant.yml ## freebayes @@ -243,6 +249,9 @@ freebayes: - modules/nf-core/gatk4/mergevcfs/main.nf - modules/nf-core/tabix/tabix/main.nf - subworkflows/local/bam_variant_calling_freebayes/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - tests/test_freebayes.yml ## haplotypecaller @@ -255,6 +264,7 @@ haplotypecaller: - modules/nf-core/samtools/index/main.nf - modules/nf-core/samtools/merge/main.nf - subworkflows/local/bam_merge_index_samtools/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - subworkflows/local/vcf_variant_filtering_gatk/main.nf - tests/test_haplotypecaller.yml @@ -266,6 +276,7 @@ haplotypecaller_skip_filter: - modules/nf-core/samtools/index/main.nf - modules/nf-core/samtools/merge/main.nf - subworkflows/local/bam_merge_index_samtools/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - tests/test_haplotypecaller_skip_filter.yml @@ -279,6 +290,7 @@ sentieon/haplotyper: - modules/nf-core/samtools/index/main.nf - modules/nf-core/samtools/merge/main.nf - subworkflows/local/bam_merge_index_samtools/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf - subworkflows/local/vcf_variant_filtering_gatk/main.nf - tests/test_sentieon_haplotyper.yml @@ -290,6 +302,7 @@ sentieon_haplotyper_skip_filter: - modules/nf-core/samtools/index/main.nf - modules/nf-core/samtools/merge/main.nf - subworkflows/local/bam_merge_index_samtools/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf - tests/test_sentieon_haplotyper_skip_filter.yml @@ -309,6 +322,7 @@ joint_germline: - modules/nf-core/samtools/merge/main.nf - subworkflows/local/bam_joint_calling_germline_gatk/main.nf - subworkflows/local/bam_merge_index_samtools/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - subworkflows/local/vcf_variant_filtering_gatk/main.nf - tests/test_joint_germline.yml @@ -330,8 +344,11 @@ manta: - modules/nf-core/manta/germline/main.nf - modules/nf-core/manta/somatic/main.nf - modules/nf-core/manta/tumoronly/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_germline_manta/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf - subworkflows/local/bam_variant_calling_somatic_manta/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf - tests/test_manta.yml @@ -340,7 +357,10 @@ mpileup: - conf/modules/mpileup.config - modules/nf-core/cat/cat/main.nf - modules/nf-core/samtools/mpileup/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_mpileup/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - tests/test_mpileup.yml ## msisensorpro @@ -348,6 +368,7 @@ msisensorpro: - conf/modules/msisensorpro.config - modules/nf-core/msisensorpro/msi_somatic/main.nf - modules/nf-core/msisensorpro/scan/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf - tests/test_msisensorpro.yml ## mutect2 @@ -361,7 +382,9 @@ mutect2: - modules/nf-core/gatk4/mergemutectstats/main.nf - modules/nf-core/gatk4/mergevcfs/main.nf - modules/nf-core/gatk4/mutect2/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf - subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf - tests/test_mutect2.yml @@ -371,8 +394,11 @@ strelka: - modules/nf-core/gatk4/mergevcfs/main.nf - modules/nf-core/strelka/germline/main.nf - modules/nf-core/strelka/somatic/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_single_strelka/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - tests/test_strelka.yml ## strelka_bp @@ -382,8 +408,11 @@ strelka_bp: - modules/nf-core/gatk4/mergevcfs/main.nf - modules/nf-core/manta/somatic/main.nf - modules/nf-core/strelka/somatic/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf - subworkflows/local/bam_variant_calling_somatic_manta/main.nf - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - tests/test_strelka_bp.yml ## tiddit @@ -392,8 +421,11 @@ tiddit: - modules/nf-core/svdb/merge/main.nf.nf - modules/nf-core/tabix/bgziptabix/main.nf - modules/nf-core/tiddit/sv/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_single_tiddit/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf - subworkflows/local/bam_variant_calling_somatic_tiddit/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - tests/test_tiddit.yml # annotate @@ -453,11 +485,14 @@ concatenate_vcfs: - modules/nf-core/tiddit/sv/main.nf - subworkflows/local/bam_variant_calling_deepvariant/main.nf - subworkflows/local/bam_variant_calling_freebayes/main.nf + - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_germline_manta/main.nf - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf - subworkflows/local/bam_variant_calling_mpileup/main.nf - subworkflows/local/bam_variant_calling_single_strelka/main.nf - subworkflows/local/bam_variant_calling_single_tiddit/main.nf + - subworkflows/local/bam_variant_calling_somatic_all/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - subworkflows/local/post_variantcalling/main.nf - subworkflows/local/vcf_concatenate_germline/main.nf - tests/test_concat_germline_vcfs.yml From 459e1d45b4e8b104907c537ffd824c5abc10acb4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 8 Sep 2023 10:59:51 +0200 Subject: [PATCH 3/3] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 59210b254b..316292ee0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -60,6 +60,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#1205](https://github.com/nf-core/sarek/pull/1205) - Less tests triggered - [#1214](https://github.com/nf-core/sarek/pull/1214) - Don't pass in intervals file to ControlFREEC for WGS analysis - [#1215](https://github.com/nf-core/sarek/pull/1215) - Fix `meta.id` for mutect2 tumor_only subworkflows +- [#1216](https://github.com/nf-core/sarek/pull/1216) - Better test coverage for variant calling `*_all` subworkflows ### Dependencies