Set scripts as inputs

workflow/conf/biohpc_local.config

@@ -2,23 +2,20 @@ process {
   executor = 'local'
   container = 'docker://bicf/bicfbase:1.3'
 
-  withLabel:checkDesignFile {
-    container = 'docker://bicf/python3:1.2'
+  withName:checkDesignFile {
+    container = 'docker://bicf/python3:1.3'
   }
-  withLabel:untarBCL {
+  withName:untarBCL {
   }
-  withLabel:mkfastq {
+  withName:mkfastq {
     container = 'docker://bicf/cellranger3.1.0:1.0'
   }
-  withLabel:countDesign {
+  withName:countDesign {
   }
-  withLabel:fastqc {
-    module = ['fastqc/0.11.5', 'parallel']
+  withName:fastqc {
+    container = 'docker://bicf/fastqc:1.5'
   }
-  withLabel:versions {
-    module = ['python/3.6.1-2-anaconda', 'cellranger/3.0.2', 'bcl2fastq/2.19.1', 'fastqc/0.11.5']
-  }
-  withLabel:multiqc {
+  withName:multiqc {
     container = 'docker://bicf/multiqc:1.4'
   }
 }

workflow/main.nf

@@ -8,7 +8,7 @@ main.nf
 *
 */
 
-// Define Input variables
+// Define input variables
 params.name = "run"
 params.bcl = "${baseDir}/../test_data/*.tar.gz"
 params.designFile = "${baseDir}/../test_data/design.csv"
@@ -16,7 +16,7 @@ params.outDir = "${baseDir}/output"
 params.multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
 params.references = "${baseDir}/../docs/references.md"
 
-// Define List of Files
+// Define list of files
 tarList = Channel
   .fromPath( params.bcl )
 bclCount = Channel
@@ -32,12 +32,18 @@ outDir = params.outDir
 multiqcConf = params.multiqcConf
 references = params.references
 
+// Define script files
+check_designScript = Channel.fromPath("$baseDir/scripts/check_design.py")
+untarBCLScript = Channel.fromPath("$baseDir/scripts/untarBCL.sh")
+countDesignScript = Channel.fromPath("$baseDir/scripts/countDesign.sh")
+fastqcScript = Channel.fromPath("$baseDir/scripts/fastqc.sh")
 
 process checkDesignFile {
 
   tag "${name}"
 
   input:
+    file check_designScript
     file designLocation
 
   output:
@@ -52,7 +58,7 @@ process checkDesignFile {
     if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
       mv "${designLocation}" "\${noSpaceDesign}"
     fi
-    python3 ${baseDir}/scripts/check_design.py -d \${noSpaceDesign}
+    python3 check_design.py -d \${noSpaceDesign}
     """
 
 }
@@ -63,6 +69,7 @@ process untarBCL {
   tag "${tar}"
 
   input:
+    file untarBCLScript
     file tar from tarList
 
   output:
@@ -111,6 +118,7 @@ if (bclCount.value == 1) {
     publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
 
     input:
+      file countDesignScript
       file fastqs from cellrangerCount.collect()
       file design from designCount
 
@@ -119,7 +127,7 @@ if (bclCount.value == 1) {
 
     script:
       """
-      bash ${baseDir}/scripts/countDesign.sh
+      bash countDesign.sh
       """
 
   }
@@ -132,6 +140,7 @@ process fastqc {
   tag "${bclName}"
 
   input:
+    file fastqcScript
     file fastqPaths
     val bclName
 
@@ -143,7 +152,7 @@ process fastqc {
     hostname
     ulimit -a
     find *.fastq.gz -exec mv {} ${bclName}.{} \\;
-    bash ${baseDir}/scripts/fastqc.sh
+    bash fastqc.sh
     """
 
 }