nf-core_modules/modules/gatk4/estimatelibrarycomplexity/meta.yml
Maxime U. Garcia 409af2f27c
Improve syntax/logic coherence in all gatk4 plugins (#1459)
* feat: code polishing

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* code polishing

* more code polishing

* code polishing

* tests for applybqsrspark

* fix typo

* no need to check md5sum for versions.yml

* fix: use correct syntax

* code polishing again

* add tests for markduplicatesspark

* simplify mergevcfs tests

* add tests for baserecalibratorspark

* fix: path to entry

* code polishing

* fix linting

* simplify module

* update meta.yml

* fix pair mode

* fix: MITO mode

* more tests

* fix command

* bad copy paste

* fix typos

* fix tests

* fix test

* update meta.yml

* correct versions.yml in all test.yml

* code polishing

* code polishing

* more code polishing

* fix args

* add tmpdir for all

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00

57 lines
1.5 KiB
YAML

name: gatk4_estimatelibrarycomplexity
description: Estimates the numbers of unique molecules in a sequencing library.
keywords:
- gatk4
- gatk4_estimatelibrarycomplexity
- duplication_metrics
- reporting
tools:
- gatk4:
description: Genome Analysis Toolkit (GATK4)
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us
tool_dev_url: https://github.com/broadinstitute/gatk
doi: "10.1158/1538-7445.AM2017-3590"
licence: ["Apache-2.0"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
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"
- metrics:
type: file
description: File containing metrics on the input files
pattern: "*.{metrics}"
authors:
- "@FriederikeHanssen"
- "@maxulysse"