From 7e835d11e21cb09fe0d9daac29503fa79f8b0043 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 26 Jul 2022 13:05:51 +0200 Subject: [PATCH 1/6] enable pytest with conda and singularity --- conf/test.config | 27 +++++++++ tests/test_aligner.yml | 2 +- tests/test_annotation.yml | 10 ++-- tests/test_bam_remap.yml | 2 +- tests/test_default.yml | 6 +- tests/test_gatk_spark.yml | 2 +- tests/test_markduplicates.yml | 4 +- tests/test_only_paired_VC.yml | 4 +- tests/test_pair.yml | 2 +- tests/test_prepare_recalibration.yml | 8 +-- tests/test_recalibrate.yml | 8 +-- tests/test_save_bam_mapped.yml | 2 +- tests/test_save_output_bam.yml | 4 +- tests/test_skip_markduplicates.yml | 6 +- tests/test_skip_qc.yml | 4 +- tests/test_split_fastq.yml | 2 +- tests/test_targeted.yml | 4 +- tests/test_tools.yml | 82 ++++++++++++++-------------- tests/test_tools_manually.yml | 6 +- tests/test_trimming.yml | 2 +- tests/test_umi.yml | 4 +- 21 files changed, 109 insertions(+), 82 deletions(-) diff --git a/conf/test.config b/conf/test.config index ea7b6d6e86..f434b783c6 100644 --- a/conf/test.config +++ b/conf/test.config @@ -233,3 +233,30 @@ process { ext.args = { "--info-key CNN_1D --indel-tranche 0" } } } + +// ENABLE CI containers for testing +if (System.getenv('PROFILE')) { + if ("$PROFILE" == "conda") { + params.enable_conda = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } else if ("$PROFILE" == "docker") { + docker.enabled = true + docker.userEmulation = { params.use_gatk_spark ? false : true }.call() + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + fixOwnership = true + } else if ("$PROFILE" == "singularity") { + singularity.enabled = true + singularity.autoMounts = true + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } +} diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml index 8333020154..1c00e1849e 100644 --- a/tests/test_aligner.yml +++ b/tests/test_aligner.yml @@ -1,5 +1,5 @@ - name: Run bwa-mem2 - command: nextflow run main.nf -profile test,docker --aligner bwa-mem2 --save_reference + command: nextflow run main.nf -profile test --aligner bwa-mem2 --save_reference tags: - aligner - bwa-mem2 diff --git a/tests/test_annotation.yml b/tests/test_annotation.yml index 45a68a81ce..8bcaca9033 100644 --- a/tests/test_annotation.yml +++ b/tests/test_annotation.yml @@ -1,5 +1,5 @@ - name: Run snpEff - command: nextflow run main.nf -profile test,annotation,docker --tools snpeff + command: nextflow run main.nf -profile test,annotation --tools snpeff tags: - annotation - snpeff @@ -11,7 +11,7 @@ - path: results/reports/snpeff/test/test_snpEff.csv - path: results/reports/snpeff/test/test_snpEff.genes.txt - name: Run VEP - command: nextflow run main.nf -profile test,annotation,docker --tools vep --skip_tools multiqc + command: nextflow run main.nf -profile test,annotation --tools vep --skip_tools multiqc tags: - annotation - vep @@ -20,7 +20,7 @@ - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi - path: results/reports/EnsemblVEP/test/test_VEP.summary.html - name: Run snpEff followed by VEP - command: nextflow run main.nf -profile test,annotation,docker --tools merge --skip_tools multiqc + command: nextflow run main.nf -profile test,annotation --tools merge --skip_tools multiqc tags: - annotation - merge @@ -47,7 +47,7 @@ - path: results/reports/EnsemblVEP/test/test_VEP.summary.html should_exist: false - name: Run snpEff, VEP and both consecutively - command: nextflow run main.nf -profile test,annotation,docker --tools merge,snpeff,vep --skip_tools multiqc + command: nextflow run main.nf -profile test,annotation --tools merge,snpeff,vep --skip_tools multiqc tags: - annotation - merge @@ -66,7 +66,7 @@ - path: results/reports/snpeff/test/test_snpEff.csv - path: results/reports/snpeff/test/test_snpEff.genes.txt - name: Run VEP with fasta - command: nextflow run main.nf -profile test,annotation,docker --tools vep --vep_include_fasta --skip_tools multiqc + command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --skip_tools multiqc tags: - annotation - vep diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml index 81f95a9e99..e4b098ce2d 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 + command: nextflow run main.nf -profile test,alignment_to_fastq tags: - alignment_to_fastq files: diff --git a/tests/test_default.yml b/tests/test_default.yml index ce77f6b090..89456c1ed6 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -1,5 +1,5 @@ - name: Run default pipeline - command: nextflow run main.nf -profile test,docker + command: nextflow run main.nf -profile test tags: - default - preprocessing @@ -28,7 +28,7 @@ - path: results/reports/samtools/test/test.md.cram.stats - path: results/reports/samtools/test/test.recal.cram.stats - name: Run default pipeline without intervals - command: nextflow run main.nf -profile test,no_intervals,docker + command: nextflow run main.nf -profile test,no_intervals tags: - default - no_intervals @@ -61,7 +61,7 @@ - path: results/reports/samtools/test/test.md.cram.stats - path: results/reports/samtools/test/test.recal.cram.stats - name: Run default pipeline with VC - command: nextflow run main.nf -profile test,docker --tools strelka + command: nextflow run main.nf -profile test --tools strelka tags: - default - preprocessing diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml index 02822feb87..fe2bebdbd8 100644 --- a/tests/test_gatk_spark.yml +++ b/tests/test_gatk_spark.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with gatk_spark - command: nextflow run main.nf -profile test,use_gatk_spark,docker + command: nextflow run main.nf -profile test,use_gatk_spark tags: - gatk4 - gatk4_spark diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml index 6df41f5c39..d496669faf 100644 --- a/tests/test_markduplicates.yml +++ b/tests/test_markduplicates.yml @@ -1,5 +1,5 @@ - name: Run markduplicates starting from BAM - command: nextflow run main.nf -profile test,markduplicates_bam,docker + command: nextflow run main.nf -profile test,markduplicates_bam tags: - bam - markduplicates @@ -28,7 +28,7 @@ - path: results/reports/samtools/test/test.md.cram.stats - path: results/reports/samtools/test/test.recal.cram.stats - name: Run markduplicates starting from CRAM - command: nextflow run main.nf -profile test,markduplicates_cram,docker + command: nextflow run main.nf -profile test,markduplicates_cram tags: - cram - markduplicates diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml index adecb54309..1f571d11f6 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 --only_paired_variant_calling + command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling tags: - cnvkit - somatic @@ -21,7 +21,7 @@ - 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 - name: Skip variant calling on matched normal - command: nextflow run main.nf -profile test,variantcalling_channels,docker --tools strelka --only_paired_variant_calling + command: nextflow run main.nf -profile test,variantcalling_channels --tools strelka --only_paired_variant_calling tags: - somatic - strelka diff --git a/tests/test_pair.yml b/tests/test_pair.yml index 6d1c8a7b2e..d734916bee 100644 --- a/tests/test_pair.yml +++ b/tests/test_pair.yml @@ -1,5 +1,5 @@ - name: Run default pipeline for tumor normal pair - command: nextflow run main.nf -profile test,pair,docker + command: nextflow run main.nf -profile test,pair tags: - preprocessing - tumor_normal_pair diff --git a/tests/test_prepare_recalibration.yml b/tests/test_prepare_recalibration.yml index f2c311a590..464175374b 100644 --- a/tests/test_prepare_recalibration.yml +++ b/tests/test_prepare_recalibration.yml @@ -1,5 +1,5 @@ - name: Run prepare_recalibration starting from bam - command: nextflow run main.nf -profile test,prepare_recalibration_bam,docker + command: nextflow run main.nf -profile test,prepare_recalibration_bam tags: - bam - prepare_recalibration @@ -20,7 +20,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - path: results/reports/samtools/test/test.recal.cram.stats - name: Run prepare_recalibration starting from cram - command: nextflow run main.nf -profile test,prepare_recalibration_cram,docker + command: nextflow run main.nf -profile test,prepare_recalibration_cram tags: - cram - prepare_recalibration @@ -38,7 +38,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - path: results/reports/samtools/test/test.recal.cram.stats - name: Run prepare_recalibration starting from bam and skip baserecalibration - command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr,docker --tools strelka + command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr --tools strelka tags: - bam - prepare_recalibration @@ -69,7 +69,7 @@ - path: results/reports/samtools_stats should_exist: false - name: Run prepare_recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr,docker --tools strelka + command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr --tools strelka tags: - cram - prepare_recalibration diff --git a/tests/test_recalibrate.yml b/tests/test_recalibrate.yml index fc01628e66..e8ea55f735 100644 --- a/tests/test_recalibrate.yml +++ b/tests/test_recalibrate.yml @@ -1,5 +1,5 @@ - name: Run Recalibration starting from bam - command: nextflow run main.nf -profile test,recalibrate_bam,docker + command: nextflow run main.nf -profile test,recalibrate_bam tags: - bam - recalibrate @@ -18,7 +18,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - path: results/reports/samtools/test/test.recal.cram.stats - name: Run Recalibration starting from cram - command: nextflow run main.nf -profile test,recalibrate_cram,docker + command: nextflow run main.nf -profile test,recalibrate_cram tags: - cram - recalibrate @@ -35,7 +35,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - path: results/reports/samtools/test/test.recal.cram.stats - name: Run Recalibration starting from bam and skip baserecalibration - command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr,docker --tools strelka + command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr --tools strelka tags: - bam - recalibrate @@ -74,7 +74,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - name: Run Recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr,docker --tools strelka + command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr --tools strelka tags: - cram - recalibrate diff --git a/tests/test_save_bam_mapped.yml b/tests/test_save_bam_mapped.yml index 9bd39fee5a..083b0f1eb8 100644 --- a/tests/test_save_bam_mapped.yml +++ b/tests/test_save_bam_mapped.yml @@ -1,5 +1,5 @@ - name: Run save_bam_mapped - command: nextflow run main.nf -profile test,docker --save_bam_mapped + command: nextflow run main.nf -profile test --save_bam_mapped tags: - preprocessing - save_bam_mapped diff --git a/tests/test_save_output_bam.yml b/tests/test_save_output_bam.yml index f49c8f9365..5131aa2f74 100644 --- a/tests/test_save_output_bam.yml +++ b/tests/test_save_output_bam.yml @@ -1,5 +1,5 @@ - name: Run save_output_as_bam - command: nextflow run main.nf -profile test,docker --save_output_as_bam + command: nextflow run main.nf -profile test --save_output_as_bam tags: - preprocessing - save_output_as_bam @@ -28,7 +28,7 @@ - path: results/reports/samtools/test/test.md.cram.stats - path: results/reports/samtools/test/test.recal.cram.stats - name: Run save_output_as_bam with gatk4 spark - command: nextflow run main.nf -profile test,use_gatk_spark,docker --save_output_as_bam + command: nextflow run main.nf -profile test,use_gatk_spark --save_output_as_bam tags: - preprocessing - save_output_as_bam diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index 252031face..fd0a84c50f 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with skipping MarkDuplicates - command: nextflow run main.nf -profile test,docker,skip_markduplicates + command: nextflow run main.nf -profile test,skip_markduplicates tags: - preprocessing - skip_markduplicates @@ -33,7 +33,7 @@ - path: results/csv/markduplicates_no_table.csv should_exist: false - name: Run skip markduplicates bam from step markduplicates - command: nextflow run main.nf -profile test,docker,markduplicates_bam,skip_markduplicates + command: nextflow run main.nf -profile test,markduplicates_bam,skip_markduplicates tags: - bam - preprocessing @@ -64,7 +64,7 @@ - path: results/csv/markduplicates_no_table.csv should_exist: false - name: Run skip markduplicates cram from step markduplicates - command: nextflow run main.nf -profile test,docker,markduplicates_cram,skip_markduplicates + command: nextflow run main.nf -profile test,markduplicates_cram,skip_markduplicates tags: - cram - preprocessing diff --git a/tests/test_skip_qc.yml b/tests/test_skip_qc.yml index cda8cdad9e..bab1ac4bef 100644 --- a/tests/test_skip_qc.yml +++ b/tests/test_skip_qc.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with skipping all QC steps - command: nextflow run main.nf -profile test,docker --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools + command: nextflow run main.nf -profile test --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools tags: - skip_qc - preprocessing @@ -24,7 +24,7 @@ should_exist: false - name: Run spark pipeline with skipping all QC steps - command: nextflow run main.nf -profile test,use_gatk_spark,docker --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools + command: nextflow run main.nf -profile test,use_gatk_spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools tags: - skip_qc - preprocessing diff --git a/tests/test_split_fastq.yml b/tests/test_split_fastq.yml index ce39aab1ee..a815d8cdf6 100644 --- a/tests/test_split_fastq.yml +++ b/tests/test_split_fastq.yml @@ -1,5 +1,5 @@ - name: Run split fastq module - command: nextflow run main.nf -profile test,split_fastq,docker + command: nextflow run main.nf -profile test,split_fastq tags: - split_fastq files: diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml index 23f84129b4..65f269d0b1 100644 --- a/tests/test_targeted.yml +++ b/tests/test_targeted.yml @@ -1,5 +1,5 @@ - name: Run default pipeline with target bed - command: nextflow run main.nf -profile test,targeted,docker + command: nextflow run main.nf -profile test,targeted tags: - preprocessing - targeted @@ -33,7 +33,7 @@ - path: results/reports/samtools/test/test.recal.cram.stats - name: Run intervals false pipeline - command: nextflow run main.nf -profile test,docker --intervals false + command: nextflow run main.nf -profile test --intervals false tags: - default - preprocessing diff --git a/tests/test_tools.yml b/tests/test_tools.yml index d90a0a9af3..39dc471cc0 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 + command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit tags: - cnvkit - somatic @@ -34,7 +34,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools cnvkit tags: - cnvkit - tumor_only @@ -55,7 +55,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools cnvkit tags: - cnvkit - germline @@ -77,7 +77,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec tags: - controlfreec - somatic @@ -105,7 +105,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --no_intervals -stub-run tags: - controlfreec - no_intervals @@ -139,7 +139,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools controlfreec -stub-run tags: - controlfreec - tumor_only @@ -167,7 +167,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools deepvariant tags: - deepvariant - germline @@ -189,7 +189,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --no_intervals tags: - deepvariant - germline @@ -215,7 +215,7 @@ - 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 + command: nextflow run main.nf -profile test,targeted --tools freebayes tags: - freebayes - germline @@ -258,7 +258,7 @@ - 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 + command: nextflow run main.nf -profile test --tools freebayes --no_intervals tags: - freebayes - germline @@ -301,7 +301,7 @@ - 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 + command: nextflow run main.nf -profile test,pair,targeted --tools freebayes tags: - freebayes - somatic @@ -372,7 +372,7 @@ - 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 + command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --no_intervals tags: - freebayes - somatic @@ -436,7 +436,7 @@ 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 +# command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes # tags: # - freebayes # - tumor_only @@ -446,7 +446,7 @@ # - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi # - name: Run variant calling on tumor_only sample with freebayes without intervals -# command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools freebayes --no_intervals +# command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals # tags: # - freebayes # - no_intervals @@ -457,7 +457,7 @@ # - path: results/variant_calling/freebayes/sample2/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 --step variant_calling + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling tags: - germline - haplotypecaller @@ -478,7 +478,7 @@ - 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 + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals tags: - germline - haplotypecaller @@ -503,7 +503,7 @@ - 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 + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --joint_germline true --step variant_calling tags: - germline - haplotypecaller @@ -522,7 +522,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools manta tags: - germline - manta @@ -539,7 +539,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools manta --no_intervals tags: - germline - manta @@ -560,7 +560,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools manta tags: - manta - tumor_only @@ -577,7 +577,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --no_intervals tags: - manta - no_intervals @@ -598,7 +598,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools manta tags: - manta - somatic @@ -627,7 +627,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools manta --no_intervals tags: - manta - no_intervals @@ -660,7 +660,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup tags: - tumor_only - mpileup @@ -670,7 +670,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --no_intervals tags: - tumor_only - mpileup @@ -684,7 +684,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools mpileup tags: - germline - mpileup @@ -694,7 +694,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools mpileup --no_intervals tags: - germline - mpileup @@ -708,7 +708,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 tags: - mutect2 - tumor_only @@ -733,7 +733,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --no_intervals tags: - mutect2 - no_intervals @@ -762,7 +762,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools msisensorpro tags: - msisensorpro - somatic @@ -776,7 +776,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools strelka tags: - germline - strelka @@ -795,7 +795,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals tags: - germline - strelka @@ -818,7 +818,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka tags: - strelka - tumor_only @@ -837,7 +837,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals tags: - no_intervals - strelka @@ -860,7 +860,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools strelka tags: - somatic - strelka @@ -891,7 +891,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools strelka --no_intervals tags: - no_intervals - somatic @@ -926,7 +926,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta tags: - somatic - strelkabp @@ -977,7 +977,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --no_intervals tags: - no_intervals - somatic @@ -1032,7 +1032,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_somatic --tools tiddit tags: - tiddit - somatic @@ -1060,7 +1060,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_germline --tools tiddit tags: - tiddit - germline @@ -1078,7 +1078,7 @@ - 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 + command: nextflow run main.nf -profile test,tools_tumoronly --tools tiddit tags: - tiddit - tumor_only diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index a206826ba6..ea383ddfae 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -1,5 +1,5 @@ - name: Run variant calling on somatic samples with ascat - command: nextflow run main.nf -profile test,tools_somatic_ascat,docker + command: nextflow run main.nf -profile test,tools_somatic_ascat tags: - ascat_manual - manual @@ -22,7 +22,7 @@ - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt - name: Run variant calling on somatic sample with mutect2 without intervals - command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 --no_intervals + command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --no_intervals tags: - mutect2_manual - manual @@ -53,7 +53,7 @@ - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.stats - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi - name: Run variant calling on somatic sample with mutect2 - command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 + command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 tags: - mutect2_manual - manual diff --git a/tests/test_trimming.yml b/tests/test_trimming.yml index d08c23b315..9d3b79b277 100644 --- a/tests/test_trimming.yml +++ b/tests/test_trimming.yml @@ -1,5 +1,5 @@ - name: Run trimming pipeline - command: nextflow run main.nf -profile test,trimming,docker --save_trimmed + command: nextflow run main.nf -profile test,trimming --save_trimmed tags: - trimming - preprocessing diff --git a/tests/test_umi.yml b/tests/test_umi.yml index b1fb32bdd8..697bf6d089 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -1,5 +1,5 @@ - name: Run UMI test - command: nextflow run main.nf -profile test,umi,docker + command: nextflow run main.nf -profile test,umi tags: - umi files: @@ -57,7 +57,7 @@ # - path: results/samtools/test-test_L1.unmapped_singleton.fq.gz # - name: Run UMI TSO test -# command: nextflow run main.nf -profile test,umi_tso,docker +# command: nextflow run main.nf -profile test,umi_tso # tags: # - umi_tso # - umi From 74e3a0efdec92169d8459ded24134b9151ea740d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 26 Jul 2022 13:10:40 +0200 Subject: [PATCH 2/6] default CI is run with docker --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6c427dd5fb..634fe4eb7f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -61,7 +61,7 @@ jobs: - "tumor_normal_pair" - "umi" - "variantcalling_channel" - + profile: ["docker"] steps: - name: Check out pipeline code uses: actions/checkout@v2 @@ -88,7 +88,7 @@ jobs: - name: Run pipeline with tests settings uses: Wandalen/wretry.action@v1.0.11 with: - command: pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes + command: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes attempt_limit: 3 - name: Output log on failure @@ -107,6 +107,6 @@ jobs: /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err /tmp/pytest_workflow_*/*/work + /tmp/pytest_workflow_*/**/.command.log !/tmp/pytest_workflow_*/*/work/conda !/tmp/pytest_workflow_*/*/work/singularity - /tmp/pytest_workflow_*/**/.command.log From bb09801cc528c97a7d5ea3f301084895b30394b1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 26 Jul 2022 13:36:14 +0200 Subject: [PATCH 3/6] update CHANGELOG --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bde5dea7c8..782d8a87df 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,9 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [#691](https://github.com/nf-core/sarek/pull/691) - Enable `PROFILE=conda`, `PROFILE=docker` and `PROFILE=singularity` for pytest + ### Changed - [#679](https://github.com/nf-core/sarek/pull/679) - Back to `dev` +- [#691](https://github.com/nf-core/sarek/pull/691) - To run the same pytest as before locally, use `PROFILE=docker` ### Fixed From 0a47ac1f194b2cf6a6a81fe11c1bb3e025897374 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 26 Jul 2022 13:50:20 +0200 Subject: [PATCH 4/6] add paths to check for modification cc @jfy133 --- .github/workflows/ci.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 634fe4eb7f..b44f8c25fe 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,6 +5,14 @@ on: branches: - dev pull_request: + paths: + - 'main.nf' + - 'modules.json' + - 'nextflow.config' + - 'workflows/sarek.nf' + - 'conf/**' + - 'subworkflows/**' + - 'modules/local/**' release: types: [published] From 5310f323e01f6f43e1f302381727483032ff2e45 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 26 Jul 2022 13:57:30 +0200 Subject: [PATCH 5/6] prettier --- .github/workflows/ci.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b44f8c25fe..26a2ecb562 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -6,13 +6,13 @@ on: - dev pull_request: paths: - - 'main.nf' - - 'modules.json' - - 'nextflow.config' - - 'workflows/sarek.nf' - - 'conf/**' - - 'subworkflows/**' - - 'modules/local/**' + - "main.nf" + - "modules.json" + - "nextflow.config" + - "workflows/sarek.nf" + - "conf/**" + - "subworkflows/**" + - "modules/local/**" release: types: [published] From 2fb8c0181ca777e7aeafbc173759e13dd751451f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 26 Jul 2022 14:08:43 +0200 Subject: [PATCH 6/6] will play with paths in a different PR --- .github/workflows/ci.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 26a2ecb562..634fe4eb7f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,14 +5,6 @@ on: branches: - dev pull_request: - paths: - - "main.nf" - - "modules.json" - - "nextflow.config" - - "workflows/sarek.nf" - - "conf/**" - - "subworkflows/**" - - "modules/local/**" release: types: [published]