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germline joint detect variants workflow
- #1043
#1043
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apaul7
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genome:master
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germline joint detect variants workflow
#1043
apaul7
wants to merge 35 commits into
genome:master
genome/analysis-workflows:master
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apaul7:full-joint-workflow
apaul7/analysis-workflows:full-joint-workflow
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Commits on Jul 15, 2021
add input to control full output filename
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add minimum confidence input for gatk calls
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s/all_cds/no_cds/
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add survivor merged annotsv tsv filtering
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update annotsv to version 2.3
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s/SURVIVOR/survivor/ and s/CNVnator/cnvnator/
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outputbinding change s/merged_sv_vcf/merged_vcf/
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stage secondary files in gather_to_sub_directory
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added min confidence input to genotype_gvcf step
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add annotated vcf as output
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add decompose and normalize step to joint genotype
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add gatk soft filtering
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add new normalize tool
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add gather to subdirectory tool for directories
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add bcftools view tool
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add manta_germline tool
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add joint cnvnator subworkflow
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add joint cnvkit subworkflow
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add joint sv read caller filtering
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add joint sv filtering for depth callers
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add joint detect svs subworkflows
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add joint detect snps subworkflow
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add joint detect variants
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pass annotsv_annotations input to subworkflow
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pass soft filtered annotated vcf as output
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Commits on Nov 17, 2021
remove doc line for easy to understand input
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ubuntu:xenial -> ubuntu:focal docker image
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quote parameters in script
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Commits on Dec 3, 2021
fix quotes
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move script inline cwl file
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add input option for output file basename
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Commits on Dec 6, 2021
Update definitions/subworkflows/gatk_soft_filter.cwl
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Update definitions/tools/bcftools_view.cwl
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Commits on Dec 7, 2021
add doc for output type
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Commits on Dec 9, 2021
use bash arrays to quote multiple vars
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