Merge branch 'de-containerize' into 'develop'

De containerize

See merge request !62

CHANGELOG.md

@@ -11,7 +11,6 @@
 
 **Background**
 * Add Nextflow Tower integration into CI (GHH's profile)
-* Utilize BICF docker containers
 * Update to be runnable on cloud
 * Refactor configs
 

README.md

@@ -22,7 +22,10 @@ Additionally, the pipeline is designed to work with Astrocyte Workflow System us
 
 Cloud Compatibility
 -------------------
-This pipeline is also capable of being run on AWS. To do so:
+This pipeline is also capable of being run on AWS.\
+**NOTE: This pipeline has been reverted to a non-containerized version to work on Astrocyte. Tag `containerized` for the last working containerized version which will be compatible with AWS.**
+
+To do so:
 * Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml)
 * In the aws configs in `workflow/configs/`:
   * Replace workDir with the S3 bucket generated

workflow/main.nf

@@ -78,6 +78,7 @@ process trackStart {
 process checkDesignFile {
 
   tag "${name}"
+  module 'python/3.6.1-2-anaconda'
 
   input:
     file check_designScript
@@ -114,6 +115,7 @@ process checkDesignFile {
 process untarBCL {  
 
   tag "${tar.simpleName}"
+  module 'pigz/2.4'
 
   input:
     file untarBCLScript
@@ -140,6 +142,7 @@ process mkfastq {
 
   tag "${bcl.simpleName}"
   publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
+  module 'cellranger/3.1.0:bcl2fastq/2.19.1'
 
   input:
     file versions_cellrangerScript
@@ -202,6 +205,7 @@ if (bclCount.value == 1) {
 process fastqc {
 
   tag "${bcl}"
+  module 'fastqc/0.11.5:parallel'
 
   input:
     file fastqcScript    
@@ -229,6 +233,7 @@ 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'
 
   input:
   file versionsScript
@@ -261,6 +266,7 @@ process multiqc {
 
   tag "${name}"
   publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
+  module 'multiqc/1.7'
 
   input:
     file multiqcConf
@@ -276,8 +282,8 @@ process multiqc {
     hostname
     ulimit -u 16384
     ulimit -a
-    export LC_ALL=C.UTF-8
-    export LANG=C.UTF-8
+    #export LC_ALL=C.UTF-8
+    #export LANG=C.UTF-8
     multiqc -c ${multiqcConf} .
     """
 

workflow/nextflow.config

@@ -22,32 +22,6 @@ profiles {
   }
 }
 
-process {
-  withName:checkDesignFile {
-    container = 'docker://bicf/python3:2.0.0'
-  }
-  withName:untarBCL {
-    container = 'docker://bicf/bicfbase:2.0.0'
-  }
-  withName:mkfastq {
-    container = 'docker://bicf/cellranger3.1.0:2.0.0'
-  }
-  withName:fastqc {
-    container = 'docker://bicf/fastqc:2.0.0'
-  }
-  withName:versions {
-    container = 'docker://bicf/python3:2.0.0'
-  }
-  withName:multiqc {
-    container = 'docker://bicf/multiqc:2.0.0'
-  }
-}
-
-singularity {
-  enabled = true
-  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
-}
-
 trace {
   enabled = true
   file = 'pipeline_trace.txt'