Updating to take a directory

no issue #
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>

diff --git a/RNA-Seq/cwl/RNA-seq-wf.cwl b/RNA-Seq/cwl/RNA-seq-wf.cwl
index 07386c1b5841d57c3a4316a70ab0179aa9125012..555e5e2cc1aa17875ff56141b68060af96ac5bdd 100644 (file)
--- a/RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/RNA-Seq/cwl/RNA-seq-wf.cwl
@@ -13,7 +13,7 @@ steps:
     scatter: fq
     in:
       fq:
-        valueFrom: $(inputs.fq.listing)
+        valueFrom: $(inputs.fqdir.listing)
       genome: genome
       gtf: gtf
     out: [qc_html, bam_sorted_indexed]
@@ -32,7 +32,7 @@ steps:
     run: helper/subdirs.cwl
     in:
       fq: 
-       valueFrom: $(inputs.fq.listing)
+       valueFrom: $(inputs.fqdir.listing)
       bams: alignment/bam_sorted_indexed
       qc: alignment/qc_html
     out: [dirs]
@@ -49,6 +49,7 @@ outputs:
 requirements:
   SubworkflowFeatureRequirement: {}
   ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
 
 hints:
   LoadListingRequirement:

diff --git a/RNA-Seq/cwl/helper/STAR-Align.cwl b/RNA-Seq/cwl/helper/STAR-Align.cwl
index 24a640ba5162932c7bcfcb0f1120892bfd6c73b7..fabb73a2030773da33286a896d1205775e997f9e 100755 (executable)
--- a/RNA-Seq/cwl/helper/STAR-Align.cwl
+++ b/RNA-Seq/cwl/helper/STAR-Align.cwl
@@ -19,7 +19,6 @@ inputs:
       prefix: "--genomeDir"
 
   ForwardReads:
-    format: edam:format_1930  # FASTQ
     type:
      - File
      - File[]
@@ -29,7 +28,6 @@ inputs:
       position: 1
   # If paired-end reads (like Illumina), both 1 and 2 must be provided.
   ReverseReads:
-    format: edam:format_1930  # FASTQ
     type:
      - "null"
      - File
@@ -248,8 +246,3 @@ outputs:
     type: ["null", File]
     outputBinding:
       glob: "Unmapped.out*"
-
-$namespaces:
-  edam: https://edamontology.org/
-$schemas:
-  - https://edamontology.org/EDAM_1.18.owl

diff --git a/RNA-Seq/cwl/helper/samtools_index.cwl b/RNA-Seq/cwl/helper/samtools_index.cwl
index 3ae2e9b1e1b8ef8d1680eece88d0af5aff9f57d0..5d0a2de6457a33461426c71eca9147f982213330 100755 (executable)
--- a/RNA-Seq/cwl/helper/samtools_index.cwl
+++ b/RNA-Seq/cwl/helper/samtools_index.cwl
@@ -32,11 +32,6 @@ outputs:
   bam_sorted_indexed:
     type: File
     secondaryFiles: .bai
-    format: edam:format_2572  # BAM 
     outputBinding:
       glob: $(inputs.bam_sorted.basename)
       
-$namespaces:
-  edam: https://edamontology.org/
-$schemas:
-  - https://edamontology.org/EDAM_1.18.owl