- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
gzip | Boolean | ||
repo | String (Optional) | ||
run_ids | String[] | ||
nthreads | Integer | ||
genomeDir | Directory | ||
annotation | File |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
cufflinks |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/cufflinks/cufflinks.cwl
(CommandLineTool)
|
Cufflinks: Transcriptome assembly and differential expression analysis for RNA-Seq |
Transcriptome assembly and differential expression analysis for RNA-Seq. http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html |
pfastq-dump |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/pfastq-dump/pfastq-dump.cwl
(CommandLineTool)
|
pfastq-dump: A bash implementation of parallel-fastq-dump, parallel fastq-dump wrapper |
pfastq-dump is a bash implementation of parallel-fastq-dump, parallel fastq-dump wrapper. --stdout option is additionally supported, but almost same features. It also uses -N and -X options of fastq-dump to specify blocks of data to be decompressed separately. https://github.com/inutano/pfastq-dump |
download-sra |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/download-sra/download-sra.cwl
(CommandLineTool)
|
download-sra: A simple download tool to get .sra file |
A simple download tool to get .sra file from a repository of INSDC members. https://github.com/inutano/download-sra |
star_mapping |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/star/mapping/paired_end/star_mapping_pe.cwl
(CommandLineTool)
|
STAR mapping: running mapping jobs. |
STAR: Spliced Transcripts Alignment to a Reference. https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf |
samtools_sort |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/samtools/sort/samtools_sort.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
cufflinks_result | File[] |
Permalink:
https://w3id.org/cwl/view/git/14c76e15665ef0566eae5c2be75dba7feb74a50b/workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.cwl