Workflow: kallisto_wf_pe.cwl
Fetched 2024-04-25 08:54:15 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 | ||
| index_file | File | ||
| out_dir_name | String (Optional) | ||
| bootstrap_samples | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| 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 |
| kallisto_quant |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/kallisto/quant/paired_end/kallisto_quant_pe.cwl
(CommandLineTool)
|
kallisto quant: runs the quantification algorithm |
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. https://pachterlab.github.io/kallisto/manual.html#quant |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| quant_output | Directory |
Permalink:
https://w3id.org/cwl/view/git/4e84905f265e1db212c406d34ae4db2bf565e856/workflows/kallisto/paired_end/kallisto_wf_pe.cwl
