Workflow: exomeseq-gatk4-preprocessing/v2.2.0
Fetched 2023-01-05 06:23:42 GMT
Verified with cwltool version 3.1.20221201130942
Whole Exome Sequence preprocessing using GATK4 - v2.2.0
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This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| library | String | ||
| threads | Integer | ||
| platform | String | ||
| read_pair | https://w3id.org/cwl/view/git/a243d20e040b0b4b6ed875e68c39fcaee2cd9620/types/FASTQReadPairType.yml#FASTQReadPairType | ||
| known_sites | File[] | ||
| bait_intervals | File[] (Optional) | ||
| resource_dbsnp | File | ||
| interval_padding | Integer (Optional) | ||
| reference_genome | File | ||
| target_intervals | File[] (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| preprocessing | |||
| prepare_reference_data |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| raw_variants | File |
Variants from HaplotypeCaller |
|
| haplotypes_bam | File |
BAM file containing assembled haplotypes |
|
| fastp_html_report | File |
QC/Trim report from fastp in HTML format |
|
| fastp_json_report | File |
QC/Trim report from fastp in JSON format |
|
| markduplicates_bam | File |
BAM and bai files from markduplicates |
|
| recalibrated_reads | File |
BAM file containing recalibrated reads |
|
| recalibration_table | File |
Table of recalibration |
|
| markduplicates_metrics | File |
metrics file from markduplicates |
Permalink:
https://w3id.org/cwl/view/git/a243d20e040b0b4b6ed875e68c39fcaee2cd9620/exomeseq-gatk4-preprocessing.cwl
