Revert input read handling to old version

Author: apeltzer

conf/test.config

@@ -14,7 +14,8 @@ params {
   genome = "Custom"
   //Input data
   singleEnd = false
-  reads = ['https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']
+  readPaths = [['JK2782_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
+  ]
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Mammoth_MT_Krause.fasta'
 }

main.nf

@@ -289,11 +289,32 @@ if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
  * Dump can be used for debugging purposes, e.g. using the -dump-channels operator on run
  */
 
-Channel
-    .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
-    .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nNB: Path requires at least one * wildcard!\nIf this is single-end data, please specify --singleEnd on the command line." }
-    .dump(tag:'input')
-    .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filtering }
+if(params.readPaths){
+    if(params.singleEnd){
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [file(row[1][0])]] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .dump(tag:'input')
+            .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filtering }
+            
+    } else {
+        Channel
+            .from(params.readPaths)
+            .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
+            .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+            .dump(tag:'input')
+            .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filtering }
+            
+    }
+} else {
+    Channel
+        .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
+        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nNB: Path requires at least one * wildcard!\nIf this is single-end data, please specify --singleEnd on the command line." }
+        .dump(tag:'input')
+        .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filtering }
+        
+}