Merge branch 'master' into 'develop'

Master

See merge request !60

astrocyte_pkg.yml

@@ -39,12 +39,7 @@ documentation_files:
 # A list of cluster environment modules that this workflow requires to run.
 # Specify versioned module names to ensure reproducability.
 workflow_modules:
-  - 'python/3.6.1-2-anaconda'
-  - 'cellranger/3.1.0'
-  - 'bcl2fastq/2.17.1.14'
-  - 'fastqc/0.11.5'
-  - 'parallel'
-  - 'multiqc/1.7'
+  - 'singularity/3.0.2'
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:

nextflow.config

+profiles {
+  standard {
+    includeConfig 'workflow/config/biohpc.config'
+  }
+  biohpc_local {
+    includeConfig 'workflow/config/biohpc_local.config'
+  }
+  aws_ondemand {
+    includeConfig 'workflow/config/aws_ondemand.config'
+  }
+  aws_spot {
+    includeConfig 'workflow/config/aws_spot.config'
+  }
+}
+
+trace {
+  enabled = true
+  file = 'pipeline_trace.txt'
+  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+}
+
+timeline {
+  enabled = true
+  file = 'timeline.html'
+}
+	
+report {
+  enabled = true
+  file = 'report.html'
+}
+
+tower {
+  enabled = true
+  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
+}
+
+manifest {
+  homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
+  description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
+  mainScript = 'main.nf'
+  version = '2.0.0'
+  nextflowVersion = '>=0.31.0'
+}
\ No newline at end of file

workflow/main.nf

@@ -10,8 +10,8 @@ main.nf
 
 // Define input variables
 params.name = "run"
-params.bcl = "${baseDir}/../test_data/*.tar.gz"
-params.designFile = "${baseDir}/../test_data/design.csv"
+params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz"
+params.designFile = "${baseDir}/../test_data/single1/cellranger-tiny-bcl-simple-1_2_0.csv"
 params.outDir = "${baseDir}/output"
 
 // Define list of files
@@ -58,8 +58,8 @@ process checkDesignFile {
   output:
     file("design.checked.csv") into designPaths
     file("design.checked.csv") into designCount
-    file("version_pipeline.txt") into version_pipeline
-    file("version_nextflow.txt") into version_nextflow
+    //file("version_pipeline.txt") into version_pipeline
+    //file("version_nextflow.txt") into version_nextflow
     file("version_python.txt") into version_python
 
   script:
@@ -71,13 +71,14 @@ process checkDesignFile {
       mv "${designLocation}" "\${noSpaceDesign}"
     fi
     python3 check_design.py -d \${noSpaceDesign}
-    echo "${workflow.manifest.version}" > version_pipeline.txt
-    echo "${workflow.nextflow.version}"> version_nextflow.txt
     bash versions_python.sh > version_python.txt
     """
 
 }
-
+/* nextflow workflow version calls that aren't compatible with nextflow 0.31.0
+    echo "${workflow.manifest.version}" > version_pipeline.txt
+    echo "${workflow.nextflow.version}" > version_nextflow.txt
+*/
 
 process untarBCL {  
 
@@ -86,7 +87,7 @@ process untarBCL {
   input:
     file untarBCLScript
     file versions_pigzScript
-    each path(tar) from tarList
+    each file(tar) from tarList
 
   output:
     file("*[!version_pigz.txt]") into bclPaths mode flatten
@@ -111,7 +112,7 @@ process mkfastq {
   input:
     file versions_cellrangerScript
     file versions_bcl2fastqScript
-    each path(bcl) from bclPaths.collect()
+    each file(bcl) from bclPaths.collect()
     file design from designPaths
 
   output:
@@ -195,8 +196,8 @@ process versions {
   input:
   file versionsScript
   file referencesScript
-  file version_pipeline
-  file version_nextflow
+  //file version_pipeline
+  //file version_nextflow
   file version_python
   file version_pigz
   file version_cellranger

workflow/scripts/generate_versions.py

@@ -26,8 +26,8 @@ logger.propagate = False
 logger.setLevel(logging.INFO)
 
 SOFTWARE_REGEX = {
-    'Pipeline': ['version_pipeline.txt', r"(\S+)"],
-    'Nextflow': ['version_nextflow.txt', r"(\S+)"],
+    #'Pipeline': ['version_pipeline.txt', r"(\S+)"],
+    #'Nextflow': ['version_nextflow.txt', r"(\S+)"],
     'python': ['version_python.txt', r"(\S+)"],
     'pigz': ['version_pigz.txt', r"(\S+)"],
     'cellranger': ['version_cellranger.txt', r"(\S+)"],
@@ -78,8 +78,8 @@ 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['cellranger'] = '<span style="color:#999999;\">N/A</span>'