From c85802da05a552f6b72f4a83d8e821e8310f9710 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 15 Jun 2023 16:06:12 +0000 Subject: [PATCH 1/4] Update public_aws_ecr profile and add test Changes: - Update public_aws_ecr profile to use mulled container - Add test for public_aws_ecr profile to "default" --- conf/public_aws_ecr.config | 3 ++ tests/test_public_aws_ecr.yml | 73 +++++++++++++++++++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 tests/test_public_aws_ecr.yml diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config index 75ff69f723..46d9e52e6b 100644 --- a/conf/public_aws_ecr.config +++ b/conf/public_aws_ecr.config @@ -55,6 +55,9 @@ process { withName: 'GATK4_CNNSCOREVARIANTS' { container = 'quay.io/nf-core/gatk:4.4.0.0' } + withName: 'GATK4_MARKDUPLICATES' { + container = 'quay.io/biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0' + } withName: 'GATK4_MARKDUPLICATES_SPARK' { container = 'quay.io/nf-core/gatk:4.4.0.0' } diff --git a/tests/test_public_aws_ecr.yml b/tests/test_public_aws_ecr.yml new file mode 100644 index 0000000000..ba800801df --- /dev/null +++ b/tests/test_public_aws_ecr.yml @@ -0,0 +1,73 @@ +- name: Run default pipeline + command: nextflow run main.nf -profile test,public_aws_ecr --outdir results + tags: + - default + - public_aws_ecr + - preprocessing + - variant_calling + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/csv/variantcalled.csv + md5sum: 4d0effd3d8dc2b814230a189e7ca9dba + - path: results/multiqc + - path: results/preprocessing/markduplicates/test/test.md.cram + # binary changes md5sums on reruns + - path: results/preprocessing/markduplicates/test/test.md.cram.crai + # binary changes md5sums on reruns + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe + - path: results/preprocessing/recalibrated/test/test.recal.cram + # binary changes md5sums on reruns + - path: results/preprocessing/recalibrated/test/test.recal.cram.crai + # binary changes md5sums on reruns + - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt + # conda changes md5sums for test + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/samtools/test/test.md.cram.stats + # conda changes md5sums for test + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test + - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary + md5sum: dd87f507da7de20d5318841af312493b + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz + # binary changes md5sums on reruns + - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi + # binary changes md5sums on reruns + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz + # binary changes md5sums on reruns + - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi + - path: results/strelka + should_exist: false + - path: results/preprocessing/mapped/ + should_exist: false From ab7b337c4a86a50e0563b4876f8c59996b0527b8 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 15 Jun 2023 16:08:45 +0000 Subject: [PATCH 2/4] CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c251401f6b..34d724460b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [#1112](https://github.com/nf-core/sarek/pull/1112) - Back to dev +- [#1113](https://github.com/nf-core/sarek/pull/1113) - Update public_aws_ecr profile and add specific test ### Changed From 8fc6419fbb2c092f548ee43be15f7be3aa4c9ec3 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 15 Jun 2023 16:29:19 +0000 Subject: [PATCH 3/4] fix test name collision --- tests/test_public_aws_ecr.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_public_aws_ecr.yml b/tests/test_public_aws_ecr.yml index ba800801df..a9abd88b42 100644 --- a/tests/test_public_aws_ecr.yml +++ b/tests/test_public_aws_ecr.yml @@ -1,4 +1,4 @@ -- name: Run default pipeline +- name: Run public_aws_ecr pipeline command: nextflow run main.nf -profile test,public_aws_ecr --outdir results tags: - default From 500d3613a80a131c52bec65b7616b9b7e52498b0 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 15 Jun 2023 17:07:58 +0000 Subject: [PATCH 4/4] Add public_aws_ecr to tags --- tests/config/tags.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/tests/config/tags.yml b/tests/config/tags.yml index 99f2cc7c7f..e5d296000f 100644 --- a/tests/config/tags.yml +++ b/tests/config/tags.yml @@ -60,6 +60,16 @@ validation_checks: - tests/test_samplesheet_validation_spaces.yml - workflows/** +public_aws_ecr: + - conf/modules/** + - main.nf + - modules/** + - nextflow.config + - nextflow_schema.json + - subworkflows/** + - tests/test_default.yml + - workflows/** + # preprocessing ## alignment_to_fastq