From 98db2b9950a87191ec3d2e2b0ee192e672ee594c Mon Sep 17 00:00:00 2001
From: veitveit <veitveit@gmail.com>
Date: Thu, 20 Jan 2022 18:02:30 +0100
Subject: [PATCH] last checks

---
 modules/maxquant/lfq/main.nf               | 8 ++++----
 modules/maxquant/lfq/meta.yml              | 8 ++++----
 tests/modules/maxquant/lfq/nextflow.config | 5 +++++
 tests/modules/maxquant/lfq/test.yml        | 1 -
 4 files changed, 13 insertions(+), 9 deletions(-)
 create mode 100644 tests/modules/maxquant/lfq/nextflow.config

diff --git a/modules/maxquant/lfq/main.nf b/modules/maxquant/lfq/main.nf
index f0210fcb..66196cbb 100644
--- a/modules/maxquant/lfq/main.nf
+++ b/modules/maxquant/lfq/main.nf
@@ -6,7 +6,7 @@ process MAXQUANT_LFQ {
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
     } else {
-	container "wombatp/maxquant-pipeline:v0.13"
+        container "wombatp/maxquant-pipeline:v0.13"
     }
 
     input:
@@ -19,10 +19,10 @@ process MAXQUANT_LFQ {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"  
-    
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
-    export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH	
+    export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH
     echo \"maxquant: \"\$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") > versions.yml
     sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
     sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
diff --git a/modules/maxquant/lfq/meta.yml b/modules/maxquant/lfq/meta.yml
index a788a888..3596e3f1 100644
--- a/modules/maxquant/lfq/meta.yml
+++ b/modules/maxquant/lfq/meta.yml
@@ -18,18 +18,18 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
 
-  - raw: 
-      type: file 
+  - raw:
+      type: file
       description: raw files with mass spectra
       pattern: "*.{raw,RAW,Raw}"
 
   - fasta:
-      type: file 
+      type: file
       description: fasta file with protein sequences
       pattern: "*.{fasta}"
 
   - parfile:
-      type: file 
+      type: file
       description: MaxQuant parameter file (XML)
       pattern: "*.{xml}"
 
diff --git a/tests/modules/maxquant/lfq/nextflow.config b/tests/modules/maxquant/lfq/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/maxquant/lfq/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/maxquant/lfq/test.yml b/tests/modules/maxquant/lfq/test.yml
index d0a7003d..5077cbc1 100644
--- a/tests/modules/maxquant/lfq/test.yml
+++ b/tests/modules/maxquant/lfq/test.yml
@@ -1,7 +1,6 @@
 ## TODO nf-core: Please run the following command to build this file:
 #                nf-core modules create-test-yml maxquant/lfq
 - name: maxquant lfq
-#  command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq --paramfile ./tests/modules/maxquant/lfq/mqpar.xml --raw 'https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_{12,14}.raw' --fasta 'https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/ABRF_iPRG_2012_target.fasta' -c tests/config/nextflow.config 
   command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq --paramfile 'https://raw.githubusercontent.com/wombat-p/DSL2-data/master/nf-core-modules/test_data/maxquant/mqpar.xml'  --fasta 'https://raw.githubusercontent.com/wombat-p/MaxQuant-Workflow/dev/data/yeast_UPS.fasta' -c tests/config/nextflow.config 
   tags:
     - maxquant