diff --git a/.github/filters.yml b/.github/filters.yml index 4337c069..b960d2b3 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -140,18 +140,18 @@ fastqc: - software/fastqc/** - tests/software/fastqc/** -gatk_createsequencedictionary: - - software/gatk/createsequencedictionary/** - - tests/software/gatk/createsequencedictionary/** +gatk4_bedtointervallist: + - software/gatk4/bedtointervallist/** + - tests/software/gatk4/bedtointervallist/** + +gatk4_createsequencedictionary: + - software/gatk4/createsequencedictionary/** + - tests/software/gatk4/createsequencedictionary/** gatk4_mergevcfs: - software/gatk4/mergevcfs/** - tests/software/gatk4/mergevcfs/** -gatk4_bedtointervallist: - - software/gatk4/bedtointervallist/** - - tests/software/gatk4/bedtointervallist/** - gatk4_revertsam: - software/gatk4/revertsam/** - tests/software/gatk4/revertsam/** diff --git a/software/gatk/createsequencedictionary/functions.nf b/software/gatk4/createsequencedictionary/functions.nf similarity index 100% rename from software/gatk/createsequencedictionary/functions.nf rename to software/gatk4/createsequencedictionary/functions.nf diff --git a/software/gatk/createsequencedictionary/main.nf b/software/gatk4/createsequencedictionary/main.nf similarity index 97% rename from software/gatk/createsequencedictionary/main.nf rename to software/gatk4/createsequencedictionary/main.nf index dd4f418c..edae4658 100644 --- a/software/gatk/createsequencedictionary/main.nf +++ b/software/gatk4/createsequencedictionary/main.nf @@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] def options = initOptions(params.options) -process GATK_CREATESEQUENCEDICTIONARY { +process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' publishDir "${params.outdir}", diff --git a/software/gatk/createsequencedictionary/meta.yml b/software/gatk4/createsequencedictionary/meta.yml similarity index 98% rename from software/gatk/createsequencedictionary/meta.yml rename to software/gatk4/createsequencedictionary/meta.yml index b192df80..b33af6ad 100644 --- a/software/gatk/createsequencedictionary/meta.yml +++ b/software/gatk4/createsequencedictionary/meta.yml @@ -1,4 +1,4 @@ -name: gatk_createsequencedictionary +name: gatk4_createsequencedictionary description: Creates a sequence dictionary for a reference sequence keywords: - dictionary diff --git a/tests/software/gatk/createsequencedictionary/main.nf b/tests/software/gatk/createsequencedictionary/main.nf deleted file mode 100644 index 46069563..00000000 --- a/tests/software/gatk/createsequencedictionary/main.nf +++ /dev/null @@ -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("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ) -} diff --git a/tests/software/gatk/createsequencedictionary/test.yml b/tests/software/gatk/createsequencedictionary/test.yml deleted file mode 100644 index e02f4604..00000000 --- a/tests/software/gatk/createsequencedictionary/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: gatk createsequencedictionary - command: nextflow run ./tests/software/gatk/createsequencedictionary -entry test_gatk_createsequencedictionary -c tests/config/nextflow.config - tags: - - gatk - - gatk_createsequencedictionary - files: - - path: ./output/gatk/test_genome.dict - md5sum: 829dd07bd0c9d3be2fd060238c0b37c3 diff --git a/tests/software/gatk4/createsequencedictionary/main.nf b/tests/software/gatk4/createsequencedictionary/main.nf new file mode 100644 index 00000000..da0427bf --- /dev/null +++ b/tests/software/gatk4/createsequencedictionary/main.nf @@ -0,0 +1,9 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../software/gatk4/createsequencedictionary/main.nf' addParams( options: [:] ) + +workflow test_gatk4_createsequencedictionary { + GATK4_CREATESEQUENCEDICTIONARY ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ) +} diff --git a/tests/software/gatk4/createsequencedictionary/test.yml b/tests/software/gatk4/createsequencedictionary/test.yml new file mode 100644 index 00000000..bbee03d7 --- /dev/null +++ b/tests/software/gatk4/createsequencedictionary/test.yml @@ -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