- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
repo | String (Optional) | ||
run_ids | String[] | ||
nthreads | Integer | ||
annotation | File | ||
genome_index_dir | Directory | ||
genome_index_base | String |
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 |
tophat2_mapping |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/tophat2/mapping/paired_end/tophat2_mapping_pe.cwl
(CommandLineTool)
|
TopHat is a fast splice junction mapper for RNA-Seq reads. [cwl for paired end] |
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. http://ccb.jhu.edu/software/tophat/index.shtml |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
cufflinks_result | File[] |
https://w3id.org/cwl/view/git/4e84905f265e1db212c406d34ae4db2bf565e856/workflows/tophat2-cufflinks/paired_end/tophat2-cufflinks_wf_pe.cwl