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

* fix: update and sort filters

* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary

.github/filters.yml

@@ -140,18 +140,18 @@ fastqc:
   - 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:
   - 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/**

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}",

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

tests/software/gatk/createsequencedictionary/main.nf

@@ -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) )
-}

tests/software/gatk/createsequencedictionary/test.yml

@@ -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

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) )
+}

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