Workflow: hisat2-stringtie_wf_se.cwl
Fetched 2023-01-12 16:40:00 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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 |
|---|---|---|---|
| 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)
|
||
| stringtie_assemble |
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/stringtie/assemble/stringtie_assemble.cwl
(CommandLineTool)
|
StringTie: Transcript assembly and quantification for RNA-Seq |
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| assemble_output | File |
https://w3id.org/cwl/view/git/85c5420fad00cc6ecefb08d3be999e82d4a69bae/workflows/hisat2-stringtie/single_end/hisat2-stringtie_wf_se.cwl
