mirror of
https://github.com/MillironX/nf-core_modules.git
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7fdeed5b79
* added template
* integrated module
* added fasta index info
* test works, have placeholder data for baits until test-data PR is merged
* added new files to config
* updated test files
* fixing fails ✨
* okay final fix here on the md5sum :face_palm:
* md5sum variable
* update meta.yml to reflect consistency to main.nf
* reverted version so conda works
* Apply suggestions from code review
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* md5sum can't be generated consistently for output
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
66 lines
1.9 KiB
YAML
66 lines
1.9 KiB
YAML
name: picard_collecthsmetrics
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description: Collects hybrid-selection (HS) metrics for a SAM or BAM file.
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keywords:
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- alignment
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- metrics
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- statistics
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- insert
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- hybrid-selection
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- quality
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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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- bam:
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type: file
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description: An aligned BAM/SAM file
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pattern: "*.{bam,sam}"
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- fasta:
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type: file
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description: |
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A reference file to calculate dropout metrics measuring reduced representation of reads.
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Optional input.
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of FASTA file. Only needed when fasta is supplied.
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pattern: "*.fai"
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- bait_intervals:
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type: file
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description: An interval list file that contains the locations of the baits used.
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pattern: "baits.interval_list"
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- target_intervals:
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type: file
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description: An interval list file that contains the locations of the targets.
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pattern: "targets.interval_list"
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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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- hs_metrics:
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type: file
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description: The metrics file.
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pattern: "*_collecthsmetrics.txt"
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authors:
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- "@projectoriented"
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