Workflow: rnaseq-alignment-quantification
Fetched 2023-01-11 13:08:24 GMT
Verified with cwltool version 3.1.20221201130942
This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| p | Boolean (Optional) | ||
| q | Integer | ||
| reads | 8ff39b43884e3d6c92704716cf6ccb7c[] | ||
| 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.cwl
(Workflow)
|
STAR-Alignment-PE |
This workflow aligns the fastq files using STAR for paired-end samples |
| 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 |
| junction_annotation |
../../tools/rseqc/rseqc-junction_annotation.cwl
(CommandLineTool)
|
RSeQC-junction_annotation |
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data |
| junction_saturation |
../../tools/rseqc/rseqc-junction_saturation.cwl
(CommandLineTool)
|
RSeQC-junction_saturation |
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 |
| gzip_junction_annotation_bed |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| gzip_junction_annotation_xls |
../../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 | ca58ec3e4ed272ea8f13a3711f0be8b4[] | ||
| gzip_gene_ent_out | File[] | ||
| gzip_gene_out_out | File[] | ||
| gzip_gene_uni_out | File[] | ||
| read_distribution_out | File[] | ||
| junction_saturation_out | File[] | ||
| gzip_transcripts_ent_out | File[] | ||
| gzip_transcripts_out_out | File[] | ||
| junction_annotation_pdf_out | 907aa40dcd6b75992f30133cbf1d03e7[] | ||
| gzip_junction_annotation_bed_out | File[] | ||
| gzip_junction_annotation_xls_out | File[] |
https://w3id.org/cwl/view/git/8967e816cb89dd9349c8c6deff686aeb8b118f1c/workflows/RNA-Seq/rnaseq-alignment-quantification.cwl
