Workflow: rnaseq-alignment-quantification-nosplice
Fetched 2023-10-21 17:35:16 GMT
Verified with cwltool version 3.1.20230201224320
This workflow QC, alignment and quantification from TPMCalculator for not spliced genomes
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| p | Boolean (Optional) | ||
| q | Integer | ||
| reads | e33a8b33e62efa0e3ab93c98a737afe8[] | ||
| threads | Integer | ||
| genomeDir | Directory | ||
| genome_bed | File | ||
| genome_gtf | File | ||
| ramMaxSTAR | Float (Optional) | ||
| ramMaxRSeQC | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bam_stat |
../../tools/rseqc/rseqc-bam_stat.cwl
(CommandLineTool)
|
RSeQC-bam_stat |
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data |
| alignment |
../Alignments/star-alignment-nosplice.cwl
(Workflow)
|
STAR-Alignment-PE |
This workflow aligns the fastq files using STAR for no spliced genomes |
| read_quality |
../../tools/rseqc/rseqc-read_quality.cwl
(CommandLineTool)
|
RSeQC-read_quality |
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data |
| gzip_gene_ent |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| gzip_gene_out |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| gzip_gene_uni |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| quantification |
../../tools/tpmcalculator/tpmcalculator.cwl
(CommandLineTool)
|
TPMCalculator |
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files |
| infer_experiment |
../../tools/rseqc/rseqc-infer_experiment.cwl
(CommandLineTool)
|
RSeQC-infer_experiment |
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data |
| read_distribution |
../../tools/rseqc/rseqc-read_distribution.cwl
(CommandLineTool)
|
RSeQC-read_distribution |
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data |
| gzip_transcripts_ent |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| gzip_transcripts_out |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stats_bam | File[] | ||
| sorted_bam | File[] | ||
| star_stats | File[] (Optional) | ||
| indexed_bam | File[] | ||
| bam_stat_out | File[] | ||
| readspergene | File[] (Optional) | ||
| experiment_out | File[] | ||
| read_quality_out | 7937cf4b6a767e7eada95f6197290805[] | ||
| gzip_gene_ent_out | File[] | ||
| gzip_gene_out_out | File[] | ||
| gzip_gene_uni_out | File[] | ||
| read_distribution_out | File[] | ||
| gzip_transcripts_ent_out | File[] | ||
| gzip_transcripts_out_out | File[] |
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/RNA-Seq/rnaseq-alignment-quantification_nosplice.cwl
