Workflow: bams2gvcf.wBQSR.multisamples.cwl
Fetched 2024-05-21 21:49:19 GMT
Verified with cwltool version 3.1.20221201130942
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- Inputs/Outputs
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 |
|---|---|---|---|
| dbsnp | File |
dbSNP data file for base recalibrator |
|
| nthreads | Integer |
number of cpu cores to be used |
|
| reference | File [FASTA] |
FastA file for reference genome |
|
| onek_indel | File |
Onek indel data file for base recalibrator |
|
| mills_indel | File |
Mills indel data file for base recalibrator |
|
| inputSamples | b55e34ba6953099ae437f504d280eb44[] | ||
| reference_interval_list_chrX | File |
interval list for reference genome (chrX) |
|
| reference_interval_list_chrY | File |
interval list for reference genome (chrY) |
|
| reference_interval_name_chrX | String |
interval name for reference genome (chrX) |
|
| reference_interval_name_chrY | String |
interval name for reference genome (chrY) |
|
| reference_interval_list_autosome | File |
interval list for reference genome (autosome) |
|
| reference_interval_name_autosome | String |
interval name for reference genome (autosome) |
Steps
There are no steps in this workflow
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| rmdup_bam | File[] | ||
| rmdup_log | File[] | ||
| rmdup_metrics | File[] | ||
| gatk3_PrintReads_log | File[] | ||
| gatk3_PrintReads_out_bam | File[] | ||
| gatk3_HaplotypeCaller_log | File[] | ||
| gatk3_HaplotypeCaller_vcf | File[] | ||
| samtools_flagstat_flagstat | File[] | ||
| samtools_idxstats_idxstats | File[] | ||
| gatk3_AnalyzeCovariates_log | File[] | ||
| gatk3_AnalyzeCovariates_bqsr_pdf | File[] | ||
| gatk3_BaseRecalibrator_after_log | File[] | ||
| gatk3_BaseRecalibrator_before_log | File[] | ||
| picard_CollectWgsMetrics_chrX_log | File[] | ||
| picard_CollectWgsMetrics_chrY_log | File[] | ||
| picard_collect_multiple_metrics_log | File[] | ||
| picard_CollectWgsMetrics_autosome_log | File[] | ||
| picard_CollectWgsMetrics_chrX_wgs_metrics | File[] | ||
| picard_CollectWgsMetrics_chrY_wgs_metrics | File[] | ||
| gatk3_BaseRecalibrator_after_bqsr_table_after | File[] | ||
| picard_CollectWgsMetrics_autosome_wgs_metrics | File[] | ||
| gatk3_BaseRecalibrator_before_bqsr_table_before | File[] [VCF] | ||
| picard_collect_multiple_metrics_insert_size_metrics | File[] | ||
| picard_collect_multiple_metrics_alignment_summary_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/a1c9cd63c80122d6a831059cdb73ec9a9455af6f/Workflows/bams2gvcf.wBQSR.multisamples.cwl
