Make script files inputs

workflow/main.nf

@@ -79,7 +79,14 @@ chemistryParam = params.chemistryParam
 version = params.version
 outDir = params.outDir
 
-// Define constant variables
+// Define script files
+check_designScript = Channel.fromPath("$baseDir/scripts/check_design.py")
+filename_checkScript = Channel.fromPath("$baseDir/scripts/filename_check.sh")
+versionsScript = Channel.fromPath("$baseDir/scripts/generate_versions.py")
+referencesScript = Channel.fromPath("$baseDir/scripts/generate_references.py")
+versions_pythonScript = Channel.fromPath("$baseDir/scripts/versions_python.sh")
+
+// Define report files
 multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
 references = "${baseDir}/../docs/references.md"
 
@@ -119,6 +126,7 @@ process checkDesignFile {
   input:
     file designLocation
     file fastqList
+    file check_designScript
 
   output:
     file("design.checked.csv") into designPaths
@@ -131,7 +139,7 @@ process checkDesignFile {
     if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
       mv "${designLocation}" "\${noSpaceDesign}"
     fi
-    python3 ${baseDir}/scripts/check_design.py -d \${noSpaceDesign} -f ${fastqList}
+    python3 check_design.py -d \${noSpaceDesign} -f ${fastqList}
     """
 }
 
@@ -179,6 +187,7 @@ process count211 {
     expectCells211
     forceCells211
     chemistryParam211
+    file filename_checkScript
 
   output:
     file("**/outs/**") into outPaths211
@@ -193,7 +202,7 @@ process count211 {
       hostname
       ulimit -u 16384
       ulimit -a
-      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      bash filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells211} --chemistry=${chemistryParam211}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
@@ -203,7 +212,7 @@ process count211 {
       hostname
       ulimit -u 16384
       ulimit -a
-      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      bash filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells211} --chemistry=${chemistryParam211}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
@@ -226,6 +235,7 @@ process count302 {
     expectCells302
     forceCells302
     chemistryParam302
+    file filename_checkScript
 
   output:
     file("**/outs/**") into outPaths302
@@ -240,7 +250,7 @@ process count302 {
       hostname
       ulimit -u 16384
       ulimit -a
-      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      bash filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells302} --chemistry=${chemistryParam302}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
@@ -250,7 +260,7 @@ process count302 {
       hostname
       ulimit -u 16384
       ulimit -a
-      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      bash filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells302} --chemistry=${chemistryParam302}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
@@ -272,6 +282,7 @@ process count310 {
     expectCells310
     forceCells310
     chemistryParam310
+    file filename_checkScript
 
   output:
     file("**/outs/**") into outPaths310
@@ -286,7 +297,7 @@ process count310 {
       hostname
       ulimit -u 16384
       ulimit -a
-      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      bash filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells310} --chemistry=${chemistryParam310}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
@@ -296,7 +307,7 @@ process count310 {
       hostname
       ulimit -u 16384
       ulimit -a
-      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      bash filename_check.sh -r ${ref}
       cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells310} --chemistry=${chemistryParam310}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
@@ -311,6 +322,8 @@ process versions {
 
   input:
     file versions_pythonScript
+    file referencesScript
+    file versions_pythonScript
 
   output:
     file("*.yaml") into yamlPaths
@@ -324,8 +337,8 @@ process versions {
     echo "${pipelineVersion}" > version_pipeline.txt
     echo "${version}" > version_cellranger.txt
     bash versions_python.sh > version_python.txt
-    python3 "${baseDir}/scripts/generate_versions.py" -f version_*.txt -o versions
-    python3 "${baseDir}/scripts/generate_references.py" -r "${references}" -o references
+    python3 generate_versions.py -f version_*.txt -o versions
+    python3 generate_references.py -r "${references}" -o references
     """
 }