Update public_aws_ecr profile and add test

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
 

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'
     }

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

tests/test_public_aws_ecr.yml

@@ -0,0 +1,73 @@
+- name: Run public_aws_ecr 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