Remove pigz version

workflow/main.nf

@@ -38,7 +38,7 @@ fastqcScript = Channel.fromPath("$baseDir/scripts/fastqc.sh")
 versionsScript = Channel.fromPath("$baseDir/scripts/generate_versions.py")
 referencesScript = Channel.fromPath("$baseDir/scripts/generate_references.py")
 versions_pythonScript = Channel.fromPath("$baseDir/scripts/versions_python.sh")
-versions_pigzScript = Channel.fromPath("$baseDir/scripts/versions_pigz.sh")
+#versions_pigzScript = Channel.fromPath("$baseDir/scripts/versions_pigz.sh")
 versions_cellrangerScript = Channel.fromPath("$baseDir/scripts/versions_cellranger.sh")
 versions_bcl2fastqScript = Channel.fromPath("$baseDir/scripts/versions_bcl2fastq.sh")
 versions_fastqcScript = Channel.fromPath("$baseDir/scripts/versions_fastqc.sh")
@@ -90,12 +90,12 @@ process untarBCL {
 
   input:
     file untarBCLScript
-    file versions_pigzScript
+    #file versions_pigzScript
     each file(tar) from tarList
 
   output:
     file("*[!version_pigz.txt]") into bclPaths mode flatten
-    file("version_pigz.txt") into version_pigz
+    #file("version_pigz.txt") into version_pigz
 
   script:
     """
@@ -103,7 +103,7 @@ process untarBCL {
     ulimit -u 16384
     ulimit -a
     bash untarBCL.sh -t ${tar}
-    bash versions_pigz.sh > version_pigz.txt
+    #bash versions_pigz.sh > version_pigz.txt
     """
 
 }

workflow/scripts/generate_versions.py

@@ -29,7 +29,7 @@ SOFTWARE_REGEX = {
     'Pipeline': ['version_pipeline.txt', r"(\S+)"],
     'Nextflow': ['version_nextflow.txt', r"(\S+)"],
     'python': ['version_python.txt', r"(\S+)"],
-    'pigz': ['version_pigz.txt', r"(\S+)"],
+    #'pigz': ['version_pigz.txt', r"(\S+)"],
     'cellranger': ['version_cellranger.txt', r"(\S+)"],
     'bcl2fastq': ['version_bcl2fastq.txt', r"(\S+)"],
     'fastqc': ['version_fastqc.txt', r"(\S+)"],
@@ -78,10 +78,10 @@ def main():
     out_filename = output + '_mqc.yaml'
 
     results = OrderedDict()
-    #results['Pipeline'] = '<span style="color:#999999;\">N/A</span>'
-    #results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
+    results['Pipeline'] = '<span style="color:#999999;\">N/A</span>'
+    results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
     results['python'] = '<span style="color:#999999;\">N/A</span>'
-    results['pigz'] = '<span style="color:#999999;\">N/A</span>'
+    #results['pigz'] = '<span style="color:#999999;\">N/A</span>'
     results['cellranger'] = '<span style="color:#999999;\">N/A</span>'
     results['bcl2fastq'] = '<span style="color:#999999;\">N/A</span>'
     results['fastqc'] = '<span style="color:#999999;\">N/A</span>'