From 813e66e6537750899fd0eda5d34b3e901d793131 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 10:54:15 +0200 Subject: [PATCH 1/4] no need for docker profile --- tests/test_aligner_sentieon_bwamem.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_aligner_sentieon_bwamem.yml b/tests/test_aligner_sentieon_bwamem.yml index 60084d0ef8..95d15ccf94 100644 --- a/tests/test_aligner_sentieon_bwamem.yml +++ b/tests/test_aligner_sentieon_bwamem.yml @@ -106,7 +106,7 @@ - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi # conda changes md5sums for test - name: Run sentieon bwamem save bam - command: nextflow run main.nf -profile test_cache,docker --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results + command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results tags: - aligner - sentieon/bwamem @@ -160,7 +160,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - name: Run sentieon bwamem save cram - command: nextflow run main.nf -profile test_cache,docker --aligner sentieon-bwamem --save_mapped --outdir results + command: nextflow run main.nf -profile test_cache --aligner sentieon-bwamem --save_mapped --outdir results tags: - aligner - sentieon/bwamem From 49f425dd8521f21fa25bc3fc64ad86a244a7e1c9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 10:54:28 +0200 Subject: [PATCH 2/4] improve test coverage --- tests/config/tags.yml | 59 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 58 insertions(+), 1 deletion(-) diff --git a/tests/config/tags.yml b/tests/config/tags.yml index ed64360a2c..851d80c225 100644 --- a/tests/config/tags.yml +++ b/tests/config/tags.yml @@ -11,6 +11,7 @@ tumor_normal_pair: - nextflow.config - nextflow_schema.json - subworkflows/** + - tests/csv/3.0/fastq_pair.csv - tests/test_tumor_normal_pair.yml - workflows/** @@ -21,6 +22,7 @@ save_mapped_only: - nextflow.config - nextflow_schema.json - subworkflows/** + - tests/csv/3.0/fastq_single.csv - tests/test_save_mapped.yml - workflows/** @@ -31,6 +33,7 @@ save_output_as_bam_only: - nextflow.config - nextflow_schema.json - subworkflows/** + - tests/csv/3.0/fastq_single.csv - tests/test_save_output_as_bam_only.yml - workflows/** @@ -41,6 +44,7 @@ skip_all_qc: - nextflow.config - nextflow_schema.json - subworkflows/** + - tests/csv/3.0/fastq_single.csv - tests/test_skip_all_qc.yml - workflows/** @@ -51,6 +55,7 @@ skip_markduplicates: - nextflow.config - nextflow_schema.json - subworkflows/** + - tests/csv/3.0/fastq_single.csv - tests/test_skip_markduplicates.yml - workflows/** @@ -61,6 +66,7 @@ validation_checks: - nextflow.config - nextflow_schema.json - subworkflows/** + - tests/csv/3.0/sample_with_space.csv - tests/test_samplesheet_validation_spaces.yml - workflows/** @@ -74,6 +80,7 @@ alignment_to_fastq: - modules/nf-core/samtools/merge/main.nf - modules/nf-core/samtools/view/main.nf - subworkflows/local/bam_convert_samtools/main.nf + - tests/csv/3.0/bam_for_remapping.csv - tests/test_alignment_to_fastq.yml ## umi @@ -89,12 +96,14 @@ umi: - modules/nf-core/samtools/bam2fq/main.nf - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf - subworkflows/local/fastq_create_umi_consensus_fgbio/main.nf + - tests/csv/3.0/fastq_umi.csv - tests/test_umi.yml ## fastp fastp: - conf/modules/trimming.config - modules/nf-core/fastp/main.nf + - tests/csv/3.0/fastq_single.csv - tests/test_fastp.yml ## aligner @@ -104,13 +113,15 @@ bwamem: - conf/modules/aligner.config - modules/nf-core/bwa/mem/main.nf - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf - - tests/test_alignment_bwamem.yml + - tests/csv/3.0/fastq_single.csv + - tests/test_aligner_bwamem.yml ### bwamem2 bwamem2: - conf/modules/aligner.config - modules/nf-core/bwamem2/mem/main.nf - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf + - tests/csv/3.0/fastq_single.csv - tests/test_aligner_bwamem2.yml ### dragmap @@ -118,6 +129,7 @@ dragmap: - conf/modules/aligner.config - modules/nf-core/dragmap/align/main.nf - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf + - tests/csv/3.0/fastq_single.csv - tests/test_aligner_dragmap.yml ### sentieon/bwamem @@ -125,6 +137,7 @@ sentieon/bwamem: - conf/modules/aligner.config - modules/nf-core/sentieon/bwamem/main.nf - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf + - tests/csv/3.0/fastq_single.csv - tests/test_aligner_sentieon_bwamem.yml ## markduplicates @@ -137,6 +150,8 @@ gatk4/markduplicates: - modules/nf-core/samtools/stats/main.nf - subworkflows/local/bam_markduplicates/main.nf - subworkflows/local/cram_qc_mosdepth_samtools/main.nf + - tests/csv/3.0/mapped_single_bam.csv + - tests/csv/3.0/mapped_single_cram.csv - tests/test_markduplicates_from_bam.yml - tests/test_markduplicates_from_cram.yml @@ -149,6 +164,8 @@ sentieon/dedup: - modules/nf-core/samtools/stats/main.nf - subworkflows/local/bam_sentieon_dedup/main.nf - subworkflows/local/cram_qc_mosdepth_samtools/main.nf + - tests/csv/3.0/mapped_single_bam.csv + - tests/csv/3.0/mapped_single_cram.csv - tests/test_sentieon_dedup_from_bam.yml - tests/test_sentieon_dedup_from_cram.yml @@ -159,6 +176,8 @@ prepare_recalibration: - modules/nf-core/gatk4/gatherbqsrreports/main.nf - modules/nf-core/samtools/convert/main.nf - subworkflows/local/bam_baserecalibrator/main.nf + - tests/csv/3.0/mapped_single_bam.csv + - tests/csv/3.0/mapped_single_cram.csv - tests/test_prepare_recalibration_from_bam.yml - tests/test_prepare_recalibration_from_cram.yml @@ -171,6 +190,8 @@ recalibrate: - modules/nf-core/samtools/merge/main.nf - subworkflows/local/bam_applybqsr/main.nf - subworkflows/local/cram_merge_index_samtools/main.nf + - tests/csv/3.0/prepare_recalibration_single_bam.csv + - tests/csv/3.0/prepare_recalibration_single_cram.csv - tests/test_recalibrate_from_bam.yml - tests/test_recalibrate_from_cram.yml @@ -182,6 +203,7 @@ intervals: - modules/nf-core/gatk4/intervallisttobed/main.nf - modules/nf-core/tabix/bgziptabix/main.nf - subworkflows/local/prepare_intervals/main.nf + - tests/csv/3.0/fastq_single.csv - tests/test_intervals.yml ## gatk4_spark @@ -196,6 +218,7 @@ gatk4_spark: - subworkflows/local/bam_applybqsr_spark/main.nf - subworkflows/local/bam_baserecalibrator_spark/main.nf - subworkflows/local/bam_markduplicates_spark/main.nf + - tests/csv/3.0/fastq_single.csv - tests/test_gatk4_spark.yml # variant calling @@ -211,6 +234,9 @@ cnvkit: - 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/csv/3.0/recalibrated_germline.csv + - tests/csv/3.0/recalibrated_somatic.csv + - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_cnvkit.yml ## controlfreec @@ -229,6 +255,8 @@ controlfreec: - 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/csv/3.0/recalibrated_somatic.csv + - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_controlfreec.yml ## deepvariant @@ -239,6 +267,7 @@ deepvariant: - 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/csv/3.0/recalibrated_germline.csv - tests/test_deepvariant.yml ## freebayes @@ -252,6 +281,9 @@ freebayes: - 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/csv/3.0/fastq_pair.csv + - tests/csv/3.0/fastq_single.csv + - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_freebayes.yml ## haplotypecaller @@ -267,6 +299,7 @@ haplotypecaller: - 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/csv/3.0/mapped_single_bam.csv - tests/test_haplotypecaller.yml haplotypecaller_skip_filter: @@ -278,6 +311,7 @@ haplotypecaller_skip_filter: - 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/csv/3.0/mapped_single_bam.csv - tests/test_haplotypecaller_skip_filter.yml ## sentieon/haplotyper @@ -293,6 +327,7 @@ sentieon/haplotyper: - 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/csv/3.0/mapped_single_bam.csv - tests/test_sentieon_haplotyper.yml sentieon_haplotyper_skip_filter: @@ -304,6 +339,7 @@ sentieon_haplotyper_skip_filter: - 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/csv/3.0/mapped_single_bam.csv - tests/test_sentieon_haplotyper_skip_filter.yml ## joint_germline @@ -325,6 +361,7 @@ joint_germline: - 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/csv/3.0/mapped_joint_bam.csv - tests/test_joint_germline.yml ## sentieon_joint_germline @@ -335,6 +372,7 @@ sentieon_joint_germline: - modules/nf-core/sentieon/haplotyper/main.nf - subworkflows/local/bam_variant_calling_germline_all/main.nf - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf + - tests/csv/3.0/mapped_joint_bam.csv - tests/test_sentieon_joint_germline.yml ## manta @@ -350,6 +388,9 @@ manta: - 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/csv/3.0/recalibrated_germline.csv + - tests/csv/3.0/recalibrated_somatic.csv + - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_manta.yml ## mpileup @@ -361,6 +402,8 @@ mpileup: - 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/csv/3.0/recalibrated_germline.csv + - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_mpileup.yml ## msisensorpro @@ -369,6 +412,7 @@ msisensorpro: - 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/csv/3.0/recalibrated_somatic.csv - tests/test_msisensorpro.yml ## mutect2 @@ -386,6 +430,7 @@ mutect2: - 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/csv/3.0/recalibrated_tumoronly.csv - tests/test_mutect2.yml ## strelka @@ -399,6 +444,10 @@ strelka: - 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/csv/3.0/recalibrated_germline.csv + - tests/csv/3.0/recalibrated_somatic.csv + - tests/csv/3.0/recalibrated_tumoronly.csv + - tests/csv/3.0/recalibrated.csv - tests/test_strelka.yml ## strelka_bp @@ -413,6 +462,7 @@ strelka_bp: - 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/csv/3.0/recalibrated_somatic.csv - tests/test_strelka_bp.yml ## tiddit @@ -426,6 +476,9 @@ tiddit: - 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/csv/3.0/recalibrated_germline.csv + - tests/csv/3.0/recalibrated_somatic.csv + - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_tiddit.yml # annotate @@ -447,6 +500,7 @@ merge: - subworkflows/local/vcf_annotate_all/main.nf - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf - subworkflows/nf-core/vcf_annotate_snpeff/main.nf + - tests/csv/3.0/vcf_single.csv - tests/test_annotation_merge.yml ## snpeff @@ -455,6 +509,7 @@ snpeff: - modules/nf-core/snpeff/snpeff/main.nf - modules/nf-core/tabix/bgziptabix/main.nf - subworkflows/nf-core/vcf_annotate_snpeff/main.nf + - tests/csv/3.0/vcf_single.csv - tests/test_annotation_snpeff.yml ## vep @@ -463,6 +518,7 @@ vep: - modules/nf-core/ensemblvep/vep/main.nf - modules/nf-core/tabix/bgziptabix/main.nf - subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf + - tests/csv/3.0/vcf_single.csv - tests/test_annotation_vep.yml # postprocessing @@ -495,4 +551,5 @@ concatenate_vcfs: - subworkflows/local/bam_variant_calling_tumor_only_all/main.nf - subworkflows/local/post_variantcalling/main.nf - subworkflows/local/vcf_concatenate_germline/main.nf + - tests/csv/3.0/mapped_joint_bam.csv - tests/test_concat_germline_vcfs.yml From 2f164c942d78ff7de0e319665b2c32a0f87a75d1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 10:57:07 +0200 Subject: [PATCH 3/4] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 86db9aae32..53a487d80e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -63,6 +63,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#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 - [#1217](https://github.com/nf-core/sarek/pull/1217) - Fix `groupTuple` statement for mutect2 tumor_only subworkflows +- [#1224](https://github.com/nf-core/sarek/pull/1224) - Better test coverage for all tests ### Dependencies From a15fd94d347799f71c46c34cd3a11800586b7556 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 10:58:02 +0200 Subject: [PATCH 4/4] update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 53a487d80e..4ffe9240f5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -63,7 +63,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#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 - [#1217](https://github.com/nf-core/sarek/pull/1217) - Fix `groupTuple` statement for mutect2 tumor_only subworkflows -- [#1224](https://github.com/nf-core/sarek/pull/1224) - Better test coverage for all tests +- [#1225](https://github.com/nf-core/sarek/pull/1225) - Better test coverage for all tests ### Dependencies