misc cleanups

common-workflow-library · Apr 17, 2024 · 4cddb2f · 4cddb2f
1 parent f55d85c
commit 4cddb2f
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/bwa/BWA-Mem2-paired.cwl b/bwa/BWA-Mem2-paired.cwl
@@ -3,7 +3,7 @@ cwlVersion: v1.2
 class: Workflow
 
 label: |
-  map medium and long reads (> 100 bp) against reference genome
+  map medium and long reads (greater than 100 bp) against reference genome
 
 inputs:
   reference_genome:

diff --git a/subread/featureCounts.cwl b/subread/featureCounts.cwl
@@ -9,6 +9,12 @@ inputs:
   mapped_reads:
     type: File
     format: [ edam:format_2572, edam:format_2573 ]  # BAM or SAM
+  reads_are_paired:
+    doc: |
+      If specified, libraries are assumed to contain paired-end reads.
+    type: boolean
+    inputBinding:
+      prefix: -p
 
 baseCommand: featureCounts