setup test config

conf/base.config

@@ -52,7 +52,7 @@ process {
     memory = { check_max( 4.GB * task.attempt, 'memory' ) }
     time = { check_max( 5.h * task.attempt, 'time' ) }
   }
- withName:build_matrix {
+ withName:build_contact_maps {
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time = { check_max( 5.h * task.attempt, 'time' ) }

conf/test.config

@@ -8,12 +8,15 @@
  */
 
 params {
+
   // Limit resources so that this can run on Travis
-  max_cpus = 2
+  max_cpus = 4
   max_memory = 6.GB
-  max_time = 48.h
+  max_time = 1.h
+  
   // Input data
-    ['SRR400264_00', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R1.fastq.gz']],
-    ['SRR400264_01', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R1.fastq.gz']],
+  readPaths = [
+    ['SRR400264_00', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_00_R2.fastq.gz']],
+    ['SRR400264_01', ['https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/hic/SRR400264_01_R2.fastq.gz']]
   ]
 }

main.nf

@@ -41,8 +41,8 @@ def helpMessage() {
     nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile docker
 
     Mandatory arguments:
-      --readsPath                   Path to input data (must be surrounded with quotes)
-      --genome                      Name of iGenomes reference
+      --reads                   Path to input data (must be surrounded with quotes)
+     // --genome                      Name of iGenomes reference
       -profile                      Configuration profile to use. Can use multiple (comma separated)
                                     Available: conda, docker, singularity, awsbatch, test and more.
 
@@ -136,17 +136,34 @@ ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
 /*
  * input read files
  */
-Channel
-        .fromFilePairs( params.readPaths )
-	.ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
-        .set { raw_reads_pairs }
-
-raw_reads = Channel.create()
-raw_reads_2 = Channel.create()
-Channel
-        .fromFilePairs( params.readPaths )
-        .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
 
+if (params.readPaths){
+   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" }
+      .set { raw_reads_pairs }
+
+   raw_reads = Channel.create()
+   raw_reads_2 = Channel.create()
+
+   Channel
+      .from( params.readPaths )
+      .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
+      .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
+}else{
+   Channel
+      .fromFilePairs( params.reads )
+      .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
+      .set { raw_reads_pairs }
+
+   raw_reads = Channel.create()
+   raw_reads_2 = Channel.create()
+
+   Channel
+      .fromFilePairs( params.reads )
+      .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
+}
 
 // SPlit fastq files
 // https://www.nextflow.io/docs/latest/operator.html#splitfastq

nextflow.config

@@ -27,7 +27,7 @@ params {
   email = false
   plaintext_email = false
   help = false
-  igenomes_base = "./iGenomes"
+  //igenomes_base = "./iGenomes"
   tracedir = "${params.outdir}/pipeline_info"
   clusterOptions = false
   awsqueue = false
@@ -63,9 +63,9 @@ profiles {
 }
 
 // Load igenomes.config if required
-if(!params.igenomesIgnore){
-  includeConfig 'conf/igenomes.config'
-}
+//if(!params.igenomesIgnore){
+//  includeConfig 'conf/igenomes.config'
+//}
 
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']