Change main and scripts

workflow/main.nf

@@ -18,6 +18,7 @@ main.nf
 
 // Define input variables
 params.name = "run"
+params.ranger = "cellranger"
 params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz"
 params.designFile = "${baseDir}/../test_data/single1/cellranger-tiny-bcl-simple-1_2_0.csv"
 params.mask = ""
@@ -34,6 +35,7 @@ bclCount = Channel
 // Define regular variables
 pipelineVersion = "3.0.0_indev"
 name = params.name
+ranger = params.ranger
 designLocation = Channel
   .fromPath(params.designFile)
   .ifEmpty { exit 1, "design file not found: ${params.designFile}" }
@@ -43,13 +45,13 @@ outDir = params.outDir
 // Define script files
 check_designScript = Channel.fromPath("$baseDir/scripts/check_design.py")
 untarBCLScript = Channel.fromPath("$baseDir/scripts/untarBCL.sh")
-countDesignScript = Channel.fromPath("$baseDir/scripts/countDesign.sh")
 fastqcScript = Channel.fromPath("$baseDir/scripts/fastqc.sh")
 versionsScript = Channel.fromPath("$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("$baseDir/scripts/versions_pigz.sh")
 versions_cellrangerScript = Channel.fromPath("$baseDir/scripts/versions_cellranger.sh")
+versions_spacerangerScript = Channel.fromPath("$baseDir/scripts/versions_spaceranger.sh")
 versions_bcl2fastqScript = Channel.fromPath("$baseDir/scripts/versions_bcl2fastq.sh")
 versions_fastqcScript = Channel.fromPath("$baseDir/scripts/versions_fastqc.sh")
 
@@ -90,6 +92,7 @@ log.info """\
 BICF cellranger_mkfastq Pipeline
 ================================
 Run name        : ${params.name}
+Ranger          : ${params.ranger}
 bcl             : ${params.bcl}
 Design File     : ${params.designFile}
 Output Directory: ${params.outDir}
@@ -163,7 +166,7 @@ process untarBCL {
 }
 
 
-process mkfastq {
+process cellranger_mkfastq {
   tag "${bcl.simpleName}"
   publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
   queue '128GB,256GB,256GBv1,384GB'
@@ -178,11 +181,14 @@ process mkfastq {
   output:
     file("fq/${bcl.simpleName}/*.fastq.gz") into fastqPaths
     val "${bcl.simpleName}" into bclName
-    file("**/outs/**/*.fastq.gz") into cellrangerCount mode flatten
+    file("**/outs/**/*.fastq.gz") into rangerCount mode flatten
     file("**/outs/fastq_path/Stats/*") into bqcPaths
-    file("version_cellranger.txt") into version_cellranger
+    file("version_ranger.txt") into version_ranger
     file("version_bcl2fastq.txt") into version_bcl2fastq
 
+  when:
+    ranger == "cellranger"
+
   script:
     """
     hostname
@@ -192,32 +198,47 @@ process mkfastq {
     mkdir fq
     mkdir "fq/${bcl.simpleName}"
     find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
-    bash versions_cellranger.sh > version_cellranger.txt
+    bash versions_cellranger.sh > version_ranger.txt
     bash versions_bcl2fastq.sh > version_bcl2fastq.txt
     """
 }
 
 
-if (bclCount.value == 1) {
-  process countDesign {
-    tag "${name}"
-    publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
+process spaceranger_mkfastq {
+  tag "${bcl.simpleName}"
+  publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
+  queue '128GB,256GB,256GBv1,384GB'
+  module 'spaceranger/1.1.0:bcl2fastq/2.19.1'
+
+  input:
+    file versions_spacerangerScript
+    file versions_bcl2fastqScript
+    each file(bcl) from bclPaths.collect()
+    file design from designPaths
 
-    input:
-      file countDesignScript
-      file fastqs from cellrangerCount.collect()
-      file design from designCount
+  output:
+    file("fq/${bcl.simpleName}/*.fastq.gz") into fastqPaths
+    val "${bcl.simpleName}" into bclName
+    file("**/outs/**/*.fastq.gz") into rangerCount mode flatten
+    file("**/outs/fastq_path/Stats/*") into bqcPaths
+    file("version_ranger.txt") into version_ranger
+    file("version_bcl2fastq.txt") into version_bcl2fastq
 
-    output:
-      file("Cellranger_Count_Design.csv") into CountDesign
+  when:
+    ranger == "spaceranger"
 
-    script:
-      """
-      hostname
-      ulimit -a
-      bash countDesign.sh
-      """
-  }
+  script:
+    """
+    hostname
+    ulimit -u 16384
+    ulimit -a
+    spaceranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} ${mask}
+    mkdir fq
+    mkdir "fq/${bcl.simpleName}"
+    find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
+    bash versions_spaceranger.sh > version_ranger.txt
+    bash versions_bcl2fastq.sh > version_bcl2fastq.txt
+    """
 }
 
 
@@ -249,7 +270,7 @@ process fastqc {
 
 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'
+  module 'python/3.6.1-2-anaconda:pandoc/2.7'
 
   input:
   file versionsScript
@@ -258,7 +279,7 @@ process versions {
   file version_nextflow
   file version_python
   //file version_pigz
-  file version_cellranger
+  file version_ranger
   file version_bcl2fastq
   file version_fastqc
   file references

workflow/scripts/generate_versions.py

@@ -30,7 +30,7 @@ SOFTWARE_REGEX = {
     'Nextflow': ['version_nextflow.txt', r"(\S+)"],
     'python': ['version_python.txt', r"(\S+)"],
     #'pigz': ['version_pigz.txt', r"(\S+)"],
-    'cellranger': ['version_cellranger.txt', r"(\S+)"],
+    '10x-ranger': ['version_ranger.txt', r"(\S+)"],
     'bcl2fastq': ['version_bcl2fastq.txt', r"(\S+)"],
     'fastqc': ['version_fastqc.txt', r"(\S+)"],
 }
@@ -82,7 +82,7 @@ def main():
     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['cellranger'] = '<span style="color:#999999;\">N/A</span>'
+    results['10x-ranger'] = '<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>'
 

workflow/scripts/countDesign.sh → workflow/scripts/versions_spaceranger.sh

 #!/bin/bash
-#countDesign.sh
+#versions_spaceranger.sh
 #*
 #* --------------------------------------------------------------------------
 #* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
 #* --------------------------------------------------------------------------
 #*
 
-fastqs=($(ls *.fastq.gz))
-design=$(ls *.csv)
-sample=$(cat ${design} | tail -n +2 | cut -d ',' -f2)
-
-echo "Sample,fastq_R1,fastq_R2" > Cellranger_Count_Design.csv;
-
-for i in ${sample};
-do
-  for j in $(seq 1 ${#fastqs[@]});
-  do
-    if [[ ${fastqs[${j}-1]} == *_I* ]]; then
-      continue
-    elif [[ ${fastqs[${j}-1]} == *${i}* && ${fastqs[${j}]} == *${i}* ]]; then
-      echo "${i},${fastqs[${j}-1]},${fastqs[${j}]}" >> Cellranger_Count_Design.csv
-    fi
-  done
-done
+spaceranger mkfastq --version | grep 'spaceranger mkfastq ' | sed 's/.*(\(.*\))/\1/'