Workflow: RNA-Seq alignment with qc
Fetched 2025-04-23 10:33:00 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File (Optional) | ||
| refgene | File | ||
| genomeDir | Directory | ||
| paired_end | Boolean | ||
| rsem_reference | String | ||
| annotation_file | File | ||
| input_sort_order | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fc |
../tools/subread_featurecounts.cwl
(CommandLineTool)
|
run subread v1.6.4 | |
| rsem |
../tools/rsem.cwl
(CommandLineTool)
|
run rsem v1.3.0 | |
| star |
../tools/star.cwl
(CommandLineTool)
|
run STAR v2.5.4 | |
| rseqc |
../tools/rseqc.cwl
(CommandLineTool)
|
run RSeQC v3.0.1 | |
| fastqc |
../tools/fastqc.cwl
(CommandLineTool)
|
run fastqc v0.11.8 | |
| preseq |
../tools/preseq.cwl
(CommandLineTool)
|
run preseq v2.0.3 | |
| sub_bam |
../tools/sub_bam.cwl
(CommandLineTool)
|
run summary | |
| cutadapt |
../tools/cutadapt.cwl
(CommandLineTool)
|
run cutadapt v2.6 | |
| mark_dup |
../tools/mark_duplicates_and_sort.cwl
(CommandLineTool)
|
Mark duplicates and Sort | |
| index_bam |
../tools/index_bam.cwl
(CommandLineTool)
|
samtools index | |
| rnaseq_summary |
../tools/rnaseqv4_summary.cwl
(CommandLineTool)
|
run summary |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gc_r | File | ||
| fc_log | File | ||
| gc_pdf | File | ||
| gc_xls | File | ||
| splice | File | ||
| htmlfile | File[] | ||
| rna_type | File | ||
| star_log | File | ||
| final_bam | File | ||
| frag_size | File | ||
| rsem_stat | Directory | ||
| genebody_r | File | ||
| genes_file | File | ||
| junction_r | File | ||
| qc_summary | File | ||
| zippedfile | File[] | ||
| aligned_bam | File | ||
| cutadapt_log | File | ||
| gene_name_fc | File | ||
| gene_type_fc | File | ||
| genebody_pdf | File | ||
| infer_strand | File | ||
| junction_bed | File | ||
| junction_xls | File | ||
| genebody_text | File | ||
| isoforms_file | File | ||
| junction_text | File | ||
| preseq_result | File | ||
| splice_events | File | ||
| gene_name_count | File | ||
| gene_type_count | File | ||
| splice_junction | File | ||
| transcript_file | File | ||
| unique_stranded | File | ||
| cutadapt_summary | File | ||
| inner_distance_r | File | ||
| junction_interact | File | ||
| read_distribution | File | ||
| transcriptome_bam | File | ||
| inner_distance_pdf | File | ||
| inner_distance_freq | File | ||
| inner_distance_text | File | ||
| gene_name_fc_summary | File | ||
| gene_type_fc_summary | File | ||
| mark_dup_metrices_file | File |
Permalink:
https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/pipelines/rnaseq4.cwl
