From 05cbbbadedfdc3b5c12985a3337762d9a2b72b26 Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Mon, 8 Mar 2021 14:45:46 +0100
Subject: [PATCH] Rename gatk/createsequencedictionary ->
 gatk4/createsequencedictionary (#260)

* fix: update and sort filters

* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
---
 .github/filters.yml                                | 14 +++++++-------
 .../createsequencedictionary/functions.nf          |  0
 .../createsequencedictionary/main.nf               |  2 +-
 .../createsequencedictionary/meta.yml              |  2 +-
 .../software/gatk/createsequencedictionary/main.nf |  9 ---------
 .../gatk/createsequencedictionary/test.yml         |  8 --------
 .../gatk4/createsequencedictionary/main.nf         |  9 +++++++++
 .../gatk4/createsequencedictionary/test.yml        |  8 ++++++++
 8 files changed, 26 insertions(+), 26 deletions(-)
 rename software/{gatk => gatk4}/createsequencedictionary/functions.nf (100%)
 rename software/{gatk => gatk4}/createsequencedictionary/main.nf (97%)
 rename software/{gatk => gatk4}/createsequencedictionary/meta.yml (98%)
 delete mode 100644 tests/software/gatk/createsequencedictionary/main.nf
 delete mode 100644 tests/software/gatk/createsequencedictionary/test.yml
 create mode 100644 tests/software/gatk4/createsequencedictionary/main.nf
 create mode 100644 tests/software/gatk4/createsequencedictionary/test.yml

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