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
+
label: RNAseq workflow
inputs:
- fqdir: Directory
+ fqdir:
+ type: Directory
+ loadListing: shallow_listing
genome: Directory
gtf: File
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
-
-hints:
- LoadListingRequirement:
- loadListing: shallow_listing
-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
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