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* first commit * first commit * update test.yml * update test.yml * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * add support for vcf haplotype maps * update test * update test data config, use test data * fix exit code * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * remove unused stub Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
53 lines
1.6 KiB
YAML
53 lines
1.6 KiB
YAML
name: "picard_crosscheckfingerprints"
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description: Checks that all data in the set of input files appear to come from the same individual
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keywords:
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- alignment
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- metrics
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- statistics
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- fingerprint
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- bam
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tools:
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- picard:
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description: |
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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
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data and formats such as SAM/BAM/CRAM and VCF.
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homepage: https://broadinstitute.github.io/picard/
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documentation: https://broadinstitute.github.io/picard/
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tool_dev_url: https://github.com/broadinstitute/picard/
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input1:
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type: file
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description: List containing 1 or more bam/vcf files or a file containing filepaths
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pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
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- input2:
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type: file
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description: Optional list containing 1 or more bam/vcf files or a file containing filepaths
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pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
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- haplotype_map:
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type: file
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description: Haplotype map file
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pattern: "*.{txt,vcf,vcf.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- crosscheck_metrics:
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type: file
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description: Metrics created by crosscheckfingerprints
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pattern: "*.{crosscheck_metrics.txt}"
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authors:
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- "@matthdsm"
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