Workflow: rnaseq-star-rsem-pe.cwl
Fetched 2023-01-03 20:55:33 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 |
|---|---|---|---|
| runid | String | ||
| nthreads | Integer (Optional) | ||
| genomeDir | Directory | ||
| quantMode | String | ||
| nthreads_1 | Integer | ||
| nthreads_2 | Integer | ||
| outSAMtype | String[] | ||
| split_files | Boolean (Optional) | ||
| rsem_index_dir | Directory | ||
| outFileNamePrefix | String (Optional) | ||
| rsem_index_prefix | String (Optional) | ||
| rsem_output_prefix | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fasterq_dump |
/cwl/view/git/69e7c0479af00695127e402962e1d81b6b8142df/tool/fasterq-dump/fasterq-dump.cwl
(CommandLineTool)
|
fasterq-dump: dump .sra format file to generate fastq file |
sra-toolkit: https://github.com/ncbi/sra-tools/wiki/Download-On-Demand |
| star_mapping_pe |
/cwl/view/git/69e7c0479af00695127e402962e1d81b6b8142df/tool/star/star_mapping-pe/star_mapping-pe.cwl
(CommandLineTool)
|
STAR mapping: running mapping jobs. |
STAR: Spliced Transcripts Alignment to a Reference. https://github.com/alexdobin/STAR/blob/main/doc/STARmanual.pdf |
| rsem_calculate_expression_pe |
/cwl/view/git/69e7c0479af00695127e402962e1d81b6b8142df/tool/rsem/rsem_calculate-expression-pe/rsem_calculate-expression-pe.cwl
(CommandLineTool)
|
rsem-calculate-expression: calculate expression values (BAM input version CWL) |
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stat | Directory | ||
| Log.out | File (Optional) | ||
| aligned | File | ||
| SJ.out.tab | File (Optional) | ||
| bamRemDups | File (Optional) | ||
| fastqFiles | File[] | ||
| genes_result | File | ||
| mappingstats | File (Optional) | ||
| readspergene | File (Optional) | ||
| transcript_bam | File | ||
| isoforms_result | File | ||
| Log.progress.out | File (Optional) | ||
| transcriptomesam | File (Optional) | ||
| transcript_sorted_bam | File (Optional) | ||
| transcript_sorted_bam_bai | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/69e7c0479af00695127e402962e1d81b6b8142df/workflow/rna-seq/rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl
