From 8e23e1839dc01927a9af3d91ca558fb12ac5eee2 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 12 Feb 2021 17:56:51 +0100
Subject: [PATCH] Trying to fix tests

---
 software/cat/fastq/main.nf        |  4 ++--
 tests/software/cat/fastq/test.yml | 10 +++++++---
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/software/cat/fastq/main.nf b/software/cat/fastq/main.nf
index 44a06bb8..95db8d9a 100644
--- a/software/cat/fastq/main.nf
+++ b/software/cat/fastq/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
 def options    = initOptions(params.options)
@@ -8,7 +8,7 @@ process CAT_FASTQ {
     tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
diff --git a/tests/software/cat/fastq/test.yml b/tests/software/cat/fastq/test.yml
index 4c9a72fd..a3122372 100644
--- a/tests/software/cat/fastq/test.yml
+++ b/tests/software/cat/fastq/test.yml
@@ -1,17 +1,21 @@
 - name: cat fastq single-end
   command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_single_end -c tests/config/nextflow.config
   tags:
+    - cat
+    - fastq
     - cat_fastqc_single_end
   files:
-    - path: output/merged_fastq/test.merged.fastq.gz
+    - path: output/cat/test.merged.fastq.gz
       md5sum: 7f753b793e5b0872758b1574db84d767
 
 - name: cat fastq paired-end
   command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_paired_end -c tests/config/nextflow.config
   tags:
+    - cat
+    - fastq
     - cat_fastqc_paired_end
   files:
-    - path: output/merged_fastq/test_1.merged.fastq.gz
+    - path: output/cat/test_1.merged.fastq.gz
       md5sum: 7f753b793e5b0872758b1574db84d767
-    - path: output/merged_fastq/test_2.merged.fastq.gz
+    - path: output/cat/test_2.merged.fastq.gz
       md5sum: c71ff917e002b1e852916a021d52921d