test_concatenate.yml edited

nf-core · Nov 28, 2024 · 74fd353 · 74fd353
1 parent a31e7db
commit 74fd353
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Showing 2 changed files with 19 additions and 30 deletions.
diff --git a/conf/modules/post_variant_calling.config b/conf/modules/post_variant_calling.config
@@ -26,7 +26,7 @@ process {
     }
 
     withName: 'GERMLINE_VCFS_CONCAT_SORT' {
-        ext.prefix = { "${meta.id}.${meta.variantcaller}.germline" }
+        ext.prefix = { "${meta.id}.germline" }
         ext.when   = { params.concatenate_vcfs }
         publishDir = [
             mode: params.publish_dir_mode,
@@ -63,7 +63,7 @@ process {
     }
 
     withName: 'TABIX_GERMLINE_VCFS_CONCAT_SORT'{
-        ext.prefix = { "${meta.id}.${meta.variantcaller}.germline" }
+        ext.prefix = { "${meta.id}.germline" }
         ext.when   = { params.concatenate_vcfs }
         publishDir = [
             mode: params.publish_dir_mode,

diff --git a/tests/test_concat_germline_vcfs.yml b/tests/test_concat_germline_vcfs.yml
@@ -3,31 +3,20 @@
   tags:
     - concatenate_vcfs
   files:
-    - path: results/variant_calling/concat/testN/testN.deepvariant.germline.vcf.gz
-    - path: results/variant_calling/concat/testT/testT.deepvariant.germline.vcf.gz
-    - path: results/variant_calling/concat/testN/testN.deepvariant.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testT/testT.deepvariant.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testN/testN.freebayes.germline.vcf.gz
-    - path: results/variant_calling/concat/testT/testT.freebayes.germline.vcf.gz
-    - path: results/variant_calling/concat/testN/testN.freebayes.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testT/testT.freebayes.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testN/testN.haplotypecaller.germline.vcf.gz
-    - path: results/variant_calling/concat/testT/testT.haplotypecaller.germline.vcf.gz
-    - path: results/variant_calling/concat/testN/testN.haplotypecaller.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testT/testT.haplotypecaller.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testN/testN.manta.germline.vcf.gz
-    - path: results/variant_calling/concat/testT/testT.manta.germline.vcf.gz
-    - path: results/variant_calling/concat/testN/testN.manta.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testT/testT.manta.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testN/testN.mpileup.germline.vcf.gz
-    - path: results/variant_calling/concat/testT/testT.mpileup.germline.vcf.gz
-    - path: results/variant_calling/concat/testN/testN.mpileup.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testT/testT.mpileup.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testN/testN.strelka.germline.vcf.gz
-    - path: results/variant_calling/concat/testT/testT.strelka.germline.vcf.gz
-    - path: results/variant_calling/concat/testN/testN.strelka.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testT/testT.strelka.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testN/testN.tiddit.germline.vcf.gz
-    - path: results/variant_calling/concat/testT/testT.tiddit.germline.vcf.gz
-    - path: results/variant_calling/concat/testN/testN.tiddit.germline.vcf.gz.tbi
-    - path: results/variant_calling/concat/testT/testT.tiddit.germline.vcf.gz.tbi
+    - path: results/variant_calling/concat/testN/testN.germline.vcf.gz
+      # binary changes md5sums on reruns
+      contains:
+        [
+          "SOURCE=testN.deepvariant.vcf.gz",
+          "AB=0.167832;ABP=277.102;AC=1;AF=0.5;AN=2;AO=48;CIGAR=1X;DP=286;DPB=286;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.855;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2017;QR=9863;RO=238;RPL=0;RPP=107.241;RPPR=519.821;RPR=48;RUN=1;SAF=24;SAP=3.0103;SAR=24;SRF=119;SRP=3.0103;SRR=119;TYPE=snp;technology.illumina=1;",
+          "SOURCE=testN.freebayes.vcf.gz",
+          "SNVHPOL=7;MQ=60;",
+          "SOURCE=testN.strelka.variants.vcf.gz",
+          "SOURCE=testN.bcftools.vcf.gz",
+        ]
+    - path: results/variant_calling/concat/testT/testT.germline.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/concat/testN/testN.germline.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/concat/testT/testT.germline.vcf.gz.tbi
+    # binary changes md5sums on reruns