Updating for proper loadListing

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

diff --git a/RNA-Seq/README.md b/RNA-Seq/README.md
index 25677fd827945bc50407591ba46a3445fc323ab5..d4e3c22c2dd10314c833d6e3def48a8d4e8f0b67 100644 (file)
--- a/RNA-Seq/README.md
+++ b/RNA-Seq/README.md
@@ -5,9 +5,22 @@ Workflows are written in CWL v1.2. (https://www.commonwl.org/)
 Subdirectories are:
 * cwl - contains CWL code for the demo
 * yml - contains YML inputs for cwl demo code
-* docker - contains dockerfiles necessary to re-create any needed docker images 
 
 To run the workflow:
 
 *  arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID ./cwl/RNA-seq-wf.cwl ./yml/RNA-seq-wf.yml
 
+About the Demo:
+This demo is based on a workflow in the Introduction to RNA-seq using high-performance computing (HPC) lessons developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). The original training, which includes additional lectures about the biology of RNA-seq, can be found at here:https://github.com/hbctraining/Intro-to-rnaseq-hpc-O2. 
+
+The data used in this demo can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50499. Citation: Kenny PJ, Zhou H, Kim M, Skariah G et al. MOV10 and FMRP regulate AGO2 association with microRNA recognition elements. Cell Rep 2014 Dec 11;9(5):1729-1741. PMID: 25464849
+
+Have questions about Arvados?
+* https://arvados.org/
+* https://gitter.im/arvados/community
+
+Have questions about CWL?
+* https://www.commonwl.org/
+* https://cwl.discourse.group/
+* https://gitter.im/common-workflow-language/common-workflow-language
+

diff --git a/RNA-Seq/cwl/RNA-seq-wf.cwl b/RNA-Seq/cwl/RNA-seq-wf.cwl
index 555e5e2cc1aa17875ff56141b68060af96ac5bdd..cb00e167719a37d2f2b09c88e44fd92194f64fdd 100644 (file)
--- a/RNA-Seq/cwl/RNA-seq-wf.cwl
+++ b/RNA-Seq/cwl/RNA-seq-wf.cwl
@@ -3,7 +3,9 @@ class: Workflow
 label: RNAseq workflow 
 
 inputs:
-  fqdir: Directory 
+  fqdir: 
+    type: Directory 
+    loadListing: shallow_listing
   genome: Directory
   gtf: File
 
@@ -50,7 +52,3 @@ requirements:
   SubworkflowFeatureRequirement: {}
   ScatterFeatureRequirement: {}
   StepInputExpressionRequirement: {}
-
-hints:
-  LoadListingRequirement:
-    loadListing: shallow_listing

diff --git a/RNA-Seq/yml/RNA-seq-wf.yml b/RNA-Seq/yml/RNA-seq-wf.yml
index 19f8c541e494d60f12f7c0d7fe31a9ed6fdc08a6..828c70c08b6e3a9e1cc4546efb494c61bc4a90cb 100644 (file)
--- a/RNA-Seq/yml/RNA-seq-wf.yml
+++ b/RNA-Seq/yml/RNA-seq-wf.yml
@@ -1,13 +1,9 @@
-fq:
-  - class: File
-    location: keep:pirca-4zz18-blweknwtwyjys0i/Mov10_oe_1.subset.fq
-    format: http://edamontology.org/format_1930
-  - class: File
-    location: keep:pirca-4zz18-blweknwtwyjys0i/Mov10_oe_2.subset.fq
-    format: http://edamontology.org/format_1930
+fqdir:
+  class: Directory
+  location: keep:pirca-4zz18-blweknwtwyjys0i/
 genome:
   class: Directory
-  location: keep:pirca-4zz18-c543b5welq68g90/hg19-chr1-STAR-index
+  location: keep:pirca-4zz18-c543b5welq68g90/hg19-STAR-index
 gtf:
   class: File
   location: keep:pirca-4zz18-c543b5welq68g90/chr1-hg19_genes.gtf

diff --git a/RNA-Seq/yml/alignment.yml b/RNA-Seq/yml/alignment.yml
index 83d0e48de108bf96a56e12da19079492e8741dd1..742b47b3d2b15f9facb95a4f84ad258801c169d7 100644 (file)
--- a/RNA-Seq/yml/alignment.yml
+++ b/RNA-Seq/yml/alignment.yml
@@ -1,10 +1,9 @@
 fq:
   class: File
   location: keep:pirca-4zz18-blweknwtwyjys0i/Mov10_oe_1.subset.fq
-  format: http://edamontology.org/format_1930
 genome:
   class: Directory
-  location: keep:pirca-4zz18-c543b5welq68g90/hg19-chr1-STAR-index
+  location: keep:pirca-4zz18-c543b5welq68g90/hg19-STAR-index
 gtf:
   class: File
   location: keep:pirca-4zz18-c543b5welq68g90/chr1-hg19_genes.gtf