From 2691061efa8341166ad6518688e5e6c0fb9a8fbf Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Thu, 15 Sep 2022 18:39:31 -0400
Subject: [PATCH] Add splitDir to take Directory input

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 RNA-Seq/cwl/RNA-seq-wf.cwl      | 18 +++++++++++-------
 RNA-Seq/cwl/helper/splitDir.cwl |  9 +++++++++
 RNA-Seq/yml/RNA-seq-wf.yml      | 10 ++++++----
 3 files changed, 26 insertions(+), 11 deletions(-)
 create mode 100644 RNA-Seq/cwl/helper/splitDir.cwl

diff --git a/RNA-Seq/cwl/RNA-seq-wf.cwl b/RNA-Seq/cwl/RNA-seq-wf.cwl
index cb00e16..183bca1 100644
--- a/RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/RNA-Seq/cwl/RNA-seq-wf.cwl
@@ -1,21 +1,26 @@
 cwlVersion: v1.2
 class: Workflow
-label: RNAseq workflow 
+label: RNAseq workflow
 
 inputs:
-  fqdir: 
-    type: Directory 
+  fqdir:
+    type: Directory
     loadListing: shallow_listing
   genome: Directory
   gtf: File
 
 steps:
+  splitDir:
+    in:
+      fqdir: fqdir
+    run: helper/splitDir.cwl
+    out: [fq]
+
   alignment:
     run: helper/alignment.cwl
     scatter: fq
     in:
-      fq:
-        valueFrom: $(inputs.fqdir.listing)
+      fq: splitDir/fq
       genome: genome
       gtf: gtf
     out: [qc_html, bam_sorted_indexed]
@@ -33,8 +38,7 @@ steps:
   output-subdirs:
     run: helper/subdirs.cwl
     in:
-      fq: 
-       valueFrom: $(inputs.fqdir.listing)
+      fq: splitDir/fq
       bams: alignment/bam_sorted_indexed
       qc: alignment/qc_html
     out: [dirs]
diff --git a/RNA-Seq/cwl/helper/splitDir.cwl b/RNA-Seq/cwl/helper/splitDir.cwl
new file mode 100644
index 0000000..e8be6c3
--- /dev/null
+++ b/RNA-Seq/cwl/helper/splitDir.cwl
@@ -0,0 +1,9 @@
+cwlVersion: v1.2
+class: ExpressionTool
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+  fqdir: Directory
+outputs:
+  fq: File[]
+expression: '${return {fq: inputs.fqdir.listing};}'
diff --git a/RNA-Seq/yml/RNA-seq-wf.yml b/RNA-Seq/yml/RNA-seq-wf.yml
index 828c70c..3c3b3ae 100644
--- a/RNA-Seq/yml/RNA-seq-wf.yml
+++ b/RNA-Seq/yml/RNA-seq-wf.yml
@@ -1,10 +1,12 @@
 fqdir:
   class: Directory
-  location: keep:pirca-4zz18-blweknwtwyjys0i/
+  location: keep:1360b500543d1d0b041084a2f99d33b6+567/
+  #location: keep:pirca-4zz18-blweknwtwyjys0i/
 genome:
   class: Directory
-  location: keep:pirca-4zz18-c543b5welq68g90/hg19-STAR-index
+  location: keep:64e703acc21226ce99f3d88eacdacd0b+3159/hg19-STAR-index
+  #location: keep:pirca-4zz18-c543b5welq68g90/hg19-STAR-index
 gtf:
   class: File
-  location: keep:pirca-4zz18-c543b5welq68g90/chr1-hg19_genes.gtf
-
+  location: keep:64e703acc21226ce99f3d88eacdacd0b+3159/chr1-hg19_genes.gtf
+  #location: keep:pirca-4zz18-c543b5welq68g90/chr1-hg19_genes.gtf
-- 
2.30.2