Add runtime info

workflow/main.nf

@@ -85,8 +85,25 @@ process trackStart {
 }
 
 
-process checkDesignFile {
+log.info """\
+  
+  BICF cellranger_mkfastq Pipeline
+  ================================
+  Run name        : ${params.name}
+  bcl             : ${params.bcl}
+  Design File     : ${params.designFile}
+  Output Directory: ${params.outDir}
+  --------------------------------
+  Nextflow Version: ${workflow.nextflow.version}
+  Pipeline Version: ${pipelineVersion}
+  Session ID      : ${workflow.sessionId}
+  --------------------------------
+  Astrocyte      : ${params.astrocyte}
+  CI             : ${params.ci}
+  Development    : ${params.dev}
+  """
 
+process checkDesignFile {
   tag "${name}"
   module 'python/3.6.1-2-anaconda'
 
@@ -115,14 +132,12 @@ process checkDesignFile {
     echo "${workflow.nextflow.version}" > version_nextflow.txt
     echo "${pipelineVersion}" > version_pipeline.txt
     """
-
 }
 /* nextflow workflow manifest version calls that aren't compatible with Asrcocyte
     echo "${workflow.manifest.version}" > version_pipeline.txt
 */
 
 process untarBCL {  
-
   tag "${tar.simpleName}"
   module 'pigz/2.4'
 
@@ -148,7 +163,6 @@ process untarBCL {
 
 
 process mkfastq {
-
   tag "${bcl.simpleName}"
   publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
   queue '128GB,256GB,256GBv1,384GB'
@@ -180,14 +194,11 @@ process mkfastq {
     bash versions_cellranger.sh > version_cellranger.txt
     bash versions_bcl2fastq.sh > version_bcl2fastq.txt
     """
-
 }
 
 
 if (bclCount.value == 1) {
-
   process countDesign {
-
     tag "${name}"
     publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
 
@@ -205,14 +216,11 @@ if (bclCount.value == 1) {
       ulimit -a
       bash countDesign.sh
       """
-
   }
-
 }
 
 
 process fastqc {
-
   tag "${bcl}"
   module 'fastqc/0.11.5:parallel'
 
@@ -235,12 +243,10 @@ process fastqc {
     bash fastqc.sh
     bash versions_fastqc.sh > version_fastqc.txt
     """
-
 }
 
 
 process versions {
-
   tag "${name}"
   module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
 
@@ -266,12 +272,10 @@ process versions {
     python3 generate_versions.py -f version_*.txt -o versions
     python3 generate_references.py -r ${references} -o references
     """
-
 }
 
 
 process multiqc {
-
   tag "${name}"
   publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
   module 'multiqc/1.7'
@@ -293,5 +297,4 @@ process multiqc {
     #export LANG=C.UTF-8
     multiqc -c ${multiqcConf} .
     """
-
 }