mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
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
|
|
description: Collects hybrid-selection (HS) metrics for a SAM or BAM file.
|
|
keywords:
|
|
- alignment
|
|
- metrics
|
|
- statistics
|
|
- insert
|
|
- hybrid-selection
|
|
- quality
|
|
- bam
|
|
tools:
|
|
- picard:
|
|
description: |
|
|
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
|
|
data and formats such as SAM/BAM/CRAM and VCF.
|
|
homepage: https://broadinstitute.github.io/picard/
|
|
documentation: https://broadinstitute.github.io/picard/
|
|
tool_dev_url: https://github.com/broadinstitute/picard/
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: An aligned BAM/SAM file
|
|
pattern: "*.{bam,sam}"
|
|
- fasta:
|
|
type: file
|
|
description: |
|
|
A reference file to calculate dropout metrics measuring reduced representation of reads.
|
|
Optional input.
|
|
pattern: "*.fasta"
|
|
- fai:
|
|
type: file
|
|
description: Index of FASTA file. Only needed when fasta is supplied.
|
|
pattern: "*.fai"
|
|
- bait_intervals:
|
|
type: file
|
|
description: An interval list file that contains the locations of the baits used.
|
|
pattern: "baits.interval_list"
|
|
- target_intervals:
|
|
type: file
|
|
description: An interval list file that contains the locations of the targets.
|
|
pattern: "targets.interval_list"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- hs_metrics:
|
|
type: file
|
|
description: The metrics file.
|
|
pattern: "*_collecthsmetrics.txt"
|
|
|
|
authors:
|
|
- "@projectoriented"
|