Workflow: bams2gvcf.woBQSR_male_chrXY_wXTR.multisamples.cwl
Fetched 2025-12-14 13:16:10 GMT
Verified with cwltool version 3.1.20221201130942
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This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | ||
| reference | File [FASTA] |
FastA file for reference genome |
|
| inputSamples | 976326639d8fb463e38d164bf0924d79[] |
Steps
There are no steps in this workflow
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| rmdup_bam | File[] | ||
| rmdup_log | File[] | ||
| rmdup_metrics | File[] | ||
| bcftools_concat_vcf | File[] | ||
| bwa_mem_SE_wXTR_log | File[] | ||
| bwa_mem_SE_wXTR_sam | File[] | ||
| bcftools_index_vcf_tbi | File[] | ||
| picard_SortSam_wXTR_bam | File[] | ||
| picard_SortSam_wXTR_log | File[] | ||
| picard_MarkDuplicates_wXTR_bam | File[] | ||
| picard_MarkDuplicates_wXTR_log | File[] | ||
| picard_MarkDuplicates_wXTR_metrics | File[] | ||
| gatk3_HaplotypeCaller_Y_ploidy1_log | File[] | ||
| gatk3_HaplotypeCaller_Y_ploidy1_vcf | File[] | ||
| gatk3_HaplotypeCaller_XTR_ploidy2_log | File[] | ||
| gatk3_HaplotypeCaller_XTR_ploidy2_vcf | File[] | ||
| gatk3_HaplotypeCaller_XPAR1_ploidy2_log | File[] | ||
| gatk3_HaplotypeCaller_XPAR1_ploidy2_vcf | File[] | ||
| gatk3_HaplotypeCaller_XPAR2_ploidy2_log | File[] | ||
| gatk3_HaplotypeCaller_XPAR2_ploidy2_vcf | File[] | ||
| gatk3_HaplotypeCaller_XCORE1_ploidy1_log | File[] | ||
| gatk3_HaplotypeCaller_XCORE1_ploidy1_vcf | File[] | ||
| gatk3_HaplotypeCaller_XCORE2_ploidy1_log | File[] | ||
| gatk3_HaplotypeCaller_XCORE2_ploidy1_vcf | File[] | ||
| samtools_extract_chrXY_unmap_chrXY_fastq | File[] |
Permalink:
https://w3id.org/cwl/view/git/a1c9cd63c80122d6a831059cdb73ec9a9455af6f/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.multisamples.cwl
