gVCF joint: provide relative symlinks for reference inputs bcbio/bcbi…

…o-nextgen#2473
bcbio · Nov 27, 2018 · 328272d · 328272d
1 parent 8146478
commit 328272d
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Showing 9 changed files with 93 additions and 111 deletions.
diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json
diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl
@@ -51,10 +51,7 @@ inputs:
 - id: config__algorithm__adapters
   type:
     items:
-    - 'null'
-    - items:
-      - 'null'
-      - string
+      items: string
       type: array
     type: array
 - id: genome_resources__variation__1000g

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl b/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl
@@ -98,10 +98,7 @@ inputs:
 - id: config__algorithm__adapters
   type:
     items:
-    - 'null'
-    - items:
-      - 'null'
-      - string
+      items: string
       type: array
     type: array
 - id: config__algorithm__bam_clean
@@ -156,10 +153,7 @@ outputs:
         type: File
       - name: config__algorithm__adapters
         type:
-        - 'null'
-        - items:
-          - 'null'
-          - string
+          items: string
           type: array
       - name: rgnames__lb
         type:

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl b/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl
@@ -61,10 +61,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl b/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl
@@ -77,10 +77,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl b/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl
@@ -106,10 +106,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:

diff --git a/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl b/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl
@@ -26,10 +26,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:

diff --git a/gvcf_joint/gvcf-joint.yaml b/gvcf_joint/gvcf-joint.yaml
@@ -20,6 +20,7 @@ details:
    files: ../testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam
  - algorithm:
      aligner: bwa
+     adapters: polyx
      recalibrate: true
      variantcaller: [gatk-haplotype, strelka2]
      tools_on: [gvcf]

diff --git a/gvcf_joint/run_generate_cwl.sh b/gvcf_joint/run_generate_cwl.sh
@@ -6,5 +6,5 @@ PNAME=gvcf-joint
 rm -rf $PNAME-workflow
 bcbio_vm.py cwl --systemconfig=../bcbio_system.yaml gvcf-joint.yaml
 
-#BASEDIR=`cd .. && pwd`
-#sed -i.bak "s#$BASEDIR/testdata#../../testdata#" $PNAME-workflow/main-$PNAME-samples.json
+BASEDIR=`cd .. && pwd`
+sed -i.bak "s#$BASEDIR/testdata#../../testdata#" $PNAME-workflow/main-$PNAME-samples.json