Workflow: rnaseq-star-rsem-deseq2.cwl
Fetched 2023-01-03 19:54:40 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 |
|---|---|---|---|
| url | String | ||
| runid | String | ||
| url_1 | String | ||
| runid_1 | String | ||
| runid_2 | String | ||
| runid_3 | String | ||
| runid_4 | String | ||
| runid_5 | String | ||
| runid_6 | String | ||
| nthreads | Integer (Optional) | ||
| quantMode | String | ||
| nthreads_1 | Integer (Optional) | ||
| nthreads_2 | Integer (Optional) | ||
| nthreads_3 | Integer (Optional) | ||
| nthreads_4 | Integer (Optional) | ||
| nthreads_5 | Integer (Optional) | ||
| nthreads_6 | Integer (Optional) | ||
| outSAMtype | String[] | ||
| runThreadN | String (Optional) | ||
| SraRunTable | File | ||
| num_threads | Integer (Optional) | ||
| output_name | String | ||
| split_files | Boolean (Optional) | ||
| output_name_1 | String | ||
| reference_prefix | String | ||
| rsem_index_prefix | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| wget |
/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/tool/wget/wget.cwl
(CommandLineTool)
|
The non-interactive network downloader |
|
| gunzip |
/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/tool/gunzip/gunzip.cwl
(CommandLineTool)
|
decompression tool using Lempel-Ziv coding (LZ77) |
|
| wget_1 |
/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/tool/wget/wget.cwl
(CommandLineTool)
|
The non-interactive network downloader |
|
| gunzip_1 |
/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/tool/gunzip/gunzip.cwl
(CommandLineTool)
|
decompression tool using Lempel-Ziv coding (LZ77) |
|
| rsem_index |
/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/tool/rsem/rsem_index/rsem_index.cwl
(CommandLineTool)
|
rsem-prepare-reference: preparing reference sequences |
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.github.io/RSEM/rsem-prepare-reference.html |
| star_index |
/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/tool/star/star_index/star_index.cwl
(CommandLineTool)
|
STAR genomeGenerate: Generating genome indexes. |
STAR: Spliced Transcripts Alignment to a Reference. https://github.com/alexdobin/STAR/blob/main/doc/STARmanual.pdf |
| star_rsem_wf_pe | |||
| star_rsem_wf_pe_1 | |||
| star_rsem_wf_pe_2 | |||
| star_rsem_wf_pe_3 | |||
| star_rsem_wf_pe_4 | |||
| star_rsem_wf_pe_5 | |||
| star_rsem_wf_pe_6 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stat | Directory | ||
| output | Directory | ||
| stat_1 | Directory | ||
| stat_2 | Directory | ||
| stat_3 | Directory | ||
| stat_4 | Directory | ||
| stat_5 | Directory | ||
| stat_6 | Directory | ||
| Log.out | File (Optional) | ||
| aligned | File | ||
| Log.out_1 | File (Optional) | ||
| Log.out_2 | File (Optional) | ||
| Log.out_3 | File (Optional) | ||
| Log.out_4 | File (Optional) | ||
| Log.out_5 | File (Optional) | ||
| Log.out_6 | File (Optional) | ||
| aligned_1 | File | ||
| aligned_2 | File | ||
| aligned_3 | File | ||
| aligned_4 | File | ||
| aligned_5 | File | ||
| aligned_6 | File | ||
| starIndex | Directory | ||
| SJ.out.tab | File (Optional) | ||
| bamRemDups | File (Optional) | ||
| downloaded | File | ||
| fastqFiles | File[] | ||
| SJ.out.tab_1 | File (Optional) | ||
| SJ.out.tab_2 | File (Optional) | ||
| SJ.out.tab_3 | File (Optional) | ||
| SJ.out.tab_4 | File (Optional) | ||
| SJ.out.tab_5 | File (Optional) | ||
| SJ.out.tab_6 | File (Optional) | ||
| bamRemDups_1 | File (Optional) | ||
| bamRemDups_2 | File (Optional) | ||
| bamRemDups_3 | File (Optional) | ||
| bamRemDups_4 | File (Optional) | ||
| bamRemDups_5 | File (Optional) | ||
| bamRemDups_6 | File (Optional) | ||
| downloaded_1 | File | ||
| fastqFiles_1 | File[] | ||
| fastqFiles_2 | File[] | ||
| fastqFiles_3 | File[] | ||
| fastqFiles_4 | File[] | ||
| fastqFiles_5 | File[] | ||
| fastqFiles_6 | File[] | ||
| genes_result | File | ||
| mappingstats | File (Optional) | ||
| readspergene | File (Optional) | ||
| rsem_index_1 | Directory | ||
| genes_result_1 | File | ||
| genes_result_2 | File | ||
| genes_result_3 | File | ||
| genes_result_4 | File | ||
| genes_result_5 | File | ||
| genes_result_6 | File | ||
| mappingstats_1 | File (Optional) | ||
| mappingstats_2 | File (Optional) | ||
| mappingstats_3 | File (Optional) | ||
| mappingstats_4 | File (Optional) | ||
| mappingstats_5 | File (Optional) | ||
| mappingstats_6 | File (Optional) | ||
| readspergene_1 | File (Optional) | ||
| readspergene_2 | File (Optional) | ||
| readspergene_3 | File (Optional) | ||
| readspergene_4 | File (Optional) | ||
| readspergene_5 | File (Optional) | ||
| readspergene_6 | File (Optional) | ||
| transcript_bam | File | ||
| isoforms_result | File | ||
| Log.progress.out | File (Optional) | ||
| transcript_bam_1 | File | ||
| transcript_bam_2 | File | ||
| transcript_bam_3 | File | ||
| transcript_bam_4 | File | ||
| transcript_bam_5 | File | ||
| transcript_bam_6 | File | ||
| transcriptomesam | File (Optional) | ||
| isoforms_result_1 | File | ||
| isoforms_result_2 | File | ||
| isoforms_result_3 | File | ||
| isoforms_result_4 | File | ||
| isoforms_result_5 | File | ||
| isoforms_result_6 | File | ||
| Log.progress.out_1 | File (Optional) | ||
| Log.progress.out_2 | File (Optional) | ||
| Log.progress.out_3 | File (Optional) | ||
| Log.progress.out_4 | File (Optional) | ||
| Log.progress.out_5 | File (Optional) | ||
| Log.progress.out_6 | File (Optional) | ||
| transcriptomesam_1 | File (Optional) | ||
| transcriptomesam_2 | File (Optional) | ||
| transcriptomesam_3 | File (Optional) | ||
| transcriptomesam_4 | File (Optional) | ||
| transcriptomesam_5 | File (Optional) | ||
| transcriptomesam_6 | File (Optional) | ||
| transcript_sorted_bam | File (Optional) | ||
| transcript_sorted_bam_1 | File (Optional) | ||
| transcript_sorted_bam_2 | File (Optional) | ||
| transcript_sorted_bam_3 | File (Optional) | ||
| transcript_sorted_bam_4 | File (Optional) | ||
| transcript_sorted_bam_5 | File (Optional) | ||
| transcript_sorted_bam_6 | File (Optional) | ||
| transcript_sorted_bam_bai | File (Optional) | ||
| transcript_sorted_bam_bai_1 | File (Optional) | ||
| transcript_sorted_bam_bai_2 | File (Optional) | ||
| transcript_sorted_bam_bai_3 | File (Optional) | ||
| transcript_sorted_bam_bai_4 | File (Optional) | ||
| transcript_sorted_bam_bai_5 | File (Optional) | ||
| transcript_sorted_bam_bai_6 | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/6db4456ca7314b036e59f50910654066da99772a/workflow/rna-seq/rnaseq-star-rsem-deseq2/rnaseq-star-rsem-deseq2.cwl
