Workflow: hisat2-cufflinks_wf_se.cwl
Fetched 2024-04-18 09:05:49 GMT
Verified with cwltool version 3.1.20221201130942
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- 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 |
|---|---|---|---|
| repo | String (Optional) | ||
| run_ids | String[] | ||
| nthreads | Integer | ||
| annotation | File | ||
| hisat2_idx_basedir | Directory | ||
| hisat2_idx_basename | 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 |
| samtools_sort |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/samtools/sort/samtools_sort.cwl
(CommandLineTool)
|
||
| hisat2_mapping |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/hisat2/mapping/single_end/hisat2_mapping_se.cwl
(CommandLineTool)
|
HISAT2: graph-based alignment of next generation sequencing reads to a population of genomes [cwl for single end read] |
HISAT2: graph-based alignment of next generation sequencing reads to a population of genomes. https://ccb.jhu.edu/software/hisat2/manual.shtml#command-line |
| samtools_sam2bam |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/samtools/sam2bam/samtools_sam2bam.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cufflinks_result | File[] |
Permalink:
https://w3id.org/cwl/view/git/4e84905f265e1db212c406d34ae4db2bf565e856/workflows/hisat2-cufflinks/single_end/hisat2-cufflinks_wf_se.cwl
