From 4cddb2fa982c9a42baa6c0ebbb34ff9e70f7d289 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 17 Apr 2024 09:34:56 +0200
Subject: [PATCH] misc cleanups

---
 bwa/BWA-Mem2-paired.cwl   | 2 +-
 subread/featureCounts.cwl | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/bwa/BWA-Mem2-paired.cwl b/bwa/BWA-Mem2-paired.cwl
index ae76b836..73478b2e 100755
--- 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
index 0ef9545a..f0d7b31e 100755
--- 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