first working version of maxquant

modules/maxquant/lfq/main.nf

@@ -24,7 +24,7 @@ process MAXQUANT_LFQ {
     path raw
 
     output:
-    tuple val(meta), path("combined/txt/*.txt"), emit: maxquant_txt
+    tuple val(meta), path("*.txt"), emit: maxquant_txt
     path "*.version.txt"          , emit: version
 
     script:
@@ -37,7 +37,7 @@ process MAXQUANT_LFQ {
     sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
     sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
     mkdir temp
-  
     maxquant mqpar_changed.xml
+    mv combined/txt/*.txt .
     """
 }

tests/config/nextflow.config

@@ -7,7 +7,7 @@ params {
 
 process {
   cpus = 2
-  memory = 3.GB
+  memory = 6.GB
   time = 2.h
 }
 

tests/modules/maxquant/lfq/main.nf

@@ -5,10 +5,13 @@ nextflow.enable.dsl = 2
 include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addParams( options: [:] )
 
 workflow test_maxquant_lfq {
-    
+        
     input = [ [ id:'test' ], // meta map
-              file(params.fasta, checkIfExists: true), file(params.paramfile, checkIfExists: true) ]
-    rawfiles = file(params.raw)
+              file(params.fasta, checkIfExists: true), file(params.paramfile, checkIfExists: true) 
+            ]
 
-    MAXQUANT_LFQ ( input, rawfiles.collect())
+
+    rawfiles = [file('https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_12.raw') , file('https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_14.raw') ]
+
+    MAXQUANT_LFQ ( input, rawfiles.collect() )
 }

tests/modules/maxquant/lfq/mqpar.xml

@@ -2,7 +2,7 @@
 <MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
 	<fastaFiles>
 		<FastaFileInfo>
-			<fastaFilePath>PLACEHOLDERyeast.fasta</fastaFilePath>
+			<fastaFilePath>PLACEHOLDERyeast_UPS.fasta</fastaFilePath>
 			<identifierParseRule>&gt;([^\s]*)</identifierParseRule>
 			<descriptionParseRule>&gt;(.*)</descriptionParseRule>
 			<taxonomyParseRule></taxonomyParseRule>

tests/modules/maxquant/lfq/test.yml

@@ -1,10 +1,11 @@
 ## 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 mqpar.xml -raw '*.raw' -fasta yeast.fasta -c tests/config/nextflow.config 
+#  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 ./tests/modules/maxquant/lfq/mqpar.xml  --fasta 'https://raw.githubusercontent.com/wombat-p/MaxQuant-Workflow/dev/data/yeast_UPS.fasta' -c tests/config/nextflow.config 
   tags:
     - maxquant
     - maxquant/lfq
   files:
     - path: output/maxquant/proteinGroups.txt
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+      md5sum: 2a6461987ace82d3f593ffbd60b65442