Merge pull request #192 from jasonwalker80/fix_ref_in_no_mark_dup

Use string input for reference
genome · Aug 10, 2017 · be7e682 · be7e682
2 parents fb93fbd + 61fbe2a
commit be7e682
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Showing 4 changed files with 17 additions and 7 deletions.
diff --git a/README.md b/README.md
@@ -1,2 +1,2 @@
-# arvados_trial
-Pilot test for using the Arvados system to create new MGI cancer pipelines.
+# cancer-genomics-workflow
+CWL workflow defintions for executing MGI Cancer Genomics analysis.
diff --git a/unaligned_bam_to_bqsr/workflow.yml → ...e_data/unaligned_bam_to_bqsr/workflow.yml b/unaligned_bam_to_bqsr/workflow.yml → ...e_data/unaligned_bam_to_bqsr/workflow.yml
@@ -1,6 +1,4 @@
-reference:
-    class: File
-    path: ../GRCh38_full_analysis_set_plus_decoy_hla.fa
+reference: ../GRCh38_full_analysis_set_plus_decoy_hla.fa
 bams:
     - {class: File, path: ../input_A.bam}
     - {class: File, path: ../input_Z.bam}

diff --git a/example_data/unaligned_bam_to_bqsr/workflow_no_dup_marking.yml b/example_data/unaligned_bam_to_bqsr/workflow_no_dup_marking.yml
@@ -0,0 +1,13 @@
+reference: /gscmnt/gc2764/cad/HCC1395/toil/refseq/GRCh38DH/GRCh38_full_analysis_set_plus_decoy_hla.fa
+bams:
+    - {class: File, path: /gscmnt/gc2764/cad/instrument_data/imported/62b8ffa0d8544d48b34bb009f6f43ec7/all_sequences.bam}
+readgroups: ['@RG\tID:62b8ffa0d8544d48b34bb009f6f43ec7\tPL:ILLUMINA\tPU:HHV33BBXX-TCCGGAGA.1\tLB:H_IJ-NA12878-NA12878_K10PCRgf-lib1\tSM:H_IJ-NA12878-NA12878_K10']
+dbsnp:
+    class: File
+    path: /gscmnt/gc2764/cad/HCC1395/toil/refseq/GRCh38DH/Homo_sapiens_assembly38.dbsnp138.vcf.gz
+known_indels:
+    class: File
+    path: /gscmnt/gc2764/cad/HCC1395/toil/refseq/GRCh38DH/Homo_sapiens_assembly38.known_indels.vcf.gz
+mills:
+    class: File
+    path: /gscmnt/gc2764/cad/HCC1395/toil/refseq/GRCh38DH/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
diff --git a/unaligned_bam_to_bqsr/workflow_no_dup_marking.cwl b/unaligned_bam_to_bqsr/workflow_no_dup_marking.cwl
@@ -14,8 +14,7 @@ inputs:
     readgroups:
         type: string[]
     reference:
-        type: File
-        secondaryFiles: [.fai, .bwt, .sa, .ann, .amb, .pac, ^.dict, .alt]
+        type: string
     dbsnp:
         type: File
         secondaryFiles: [.tbi]