Workflow: rapdb-pipeline_wo_tasuke.cwl
Fetched 2023-01-11 00:06:44 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File |
FASTQ file for the forward read |
|
| fastq2 | File |
FASTQ file for the reverse read |
|
| ref_gtf | File |
Reference GTF file for snpEff |
|
| threads | Integer |
Number of threads for parallel processing |
|
| outprefix | String |
Prefix for output files |
|
| reference | File |
FASTA file for reference genome |
|
| ref_protein | File |
Reference protein FASTA for snpEff |
|
| filter-expression | String |
VCF filter condition for GATK-VariantFiltration |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| snpeff |
snpeff_all.cwl
(Workflow)
|
||
| bam2vcf |
bam2vcf.cwl
(Workflow)
|
||
| fastq2bam |
fastq2bam.cwl
(Workflow)
|
||
| prepare_reference |
prepare_reference.cwl
(Workflow)
|
||
| read_preprocessing |
read_preprocessing.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_stats | File | ||
| read_stats | File | ||
| snpeff_vcf | File | ||
| snpeff_genes | File | ||
| vcf_with_tbi | File | ||
| rmdup_metrics | File | ||
| bam_with_index | File | ||
| fastqc_result1 | File | ||
| fastqc_result2 | File | ||
| read_stats_raw | File | ||
| snpeff_summary | File | ||
| unmapped_fastq1 | File | ||
| unmapped_fastq2 | File | ||
| hc_gvcf_with_tbi | File | ||
| fastqc_raw_result1 | File | ||
| fastqc_raw_result2 | File | ||
| trimmomatic_summary | File |
Permalink:
https://w3id.org/cwl/view/git/356c47bb87dbcd9a9cb565f147b0dad298dea6cb/workflows/rapdb-pipeline_wo_tasuke.cwl
