Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary (#260)

* fix: update and sort filters

* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
This commit is contained in:
Maxime Garcia 2021-03-08 14:45:46 +01:00 committed by GitHub
parent 4566525da2
commit 05cbbbaded
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GPG key ID: 4AEE18F83AFDEB23
8 changed files with 26 additions and 26 deletions

14
.github/filters.yml vendored
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@ -140,18 +140,18 @@ fastqc:
- software/fastqc/** - software/fastqc/**
- tests/software/fastqc/** - tests/software/fastqc/**
gatk_createsequencedictionary: gatk4_bedtointervallist:
- software/gatk/createsequencedictionary/** - software/gatk4/bedtointervallist/**
- tests/software/gatk/createsequencedictionary/** - tests/software/gatk4/bedtointervallist/**
gatk4_createsequencedictionary:
- software/gatk4/createsequencedictionary/**
- tests/software/gatk4/createsequencedictionary/**
gatk4_mergevcfs: gatk4_mergevcfs:
- software/gatk4/mergevcfs/** - software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/** - tests/software/gatk4/mergevcfs/**
gatk4_bedtointervallist:
- software/gatk4/bedtointervallist/**
- tests/software/gatk4/bedtointervallist/**
gatk4_revertsam: gatk4_revertsam:
- software/gatk4/revertsam/** - software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/** - tests/software/gatk4/revertsam/**

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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:] params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
process GATK_CREATESEQUENCEDICTIONARY { process GATK4_CREATESEQUENCEDICTIONARY {
tag "$fasta" tag "$fasta"
label 'process_medium' label 'process_medium'
publishDir "${params.outdir}", publishDir "${params.outdir}",

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@ -1,4 +1,4 @@
name: gatk_createsequencedictionary name: gatk4_createsequencedictionary
description: Creates a sequence dictionary for a reference sequence description: Creates a sequence dictionary for a reference sequence
keywords: keywords:
- dictionary - dictionary

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@ -1,9 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK_CREATESEQUENCEDICTIONARY } from '../../../../software/gatk/createsequencedictionary/main.nf' addParams( options: [:] )
workflow test_gatk_createsequencedictionary {
GATK_CREATESEQUENCEDICTIONARY ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
}

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@ -1,8 +0,0 @@
- name: gatk createsequencedictionary
command: nextflow run ./tests/software/gatk/createsequencedictionary -entry test_gatk_createsequencedictionary -c tests/config/nextflow.config
tags:
- gatk
- gatk_createsequencedictionary
files:
- path: ./output/gatk/test_genome.dict
md5sum: 829dd07bd0c9d3be2fd060238c0b37c3

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@ -0,0 +1,9 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../software/gatk4/createsequencedictionary/main.nf' addParams( options: [:] )
workflow test_gatk4_createsequencedictionary {
GATK4_CREATESEQUENCEDICTIONARY ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
}

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@ -0,0 +1,8 @@
- name: gatk4 createsequencedictionary
command: nextflow run ./tests/software/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c tests/config/nextflow.config
tags:
- gatk4
- gatk4_createsequencedictionary
files:
- path: ./output/gatk4/test_genome.dict
md5sum: 829dd07bd0c9d3be2fd060238c0b37c3