Merge branch 'develop' into 'master'

Develop

See merge request !12

.gitignore

@@ -296,14 +296,17 @@ $RECYCLE.BIN/
 # End of https://www.gitignore.io/api/r,perl,macos,linux,python,windows
 
 # nextflow analysis folders/files
-/test_data/*.fastq.gz
-/test_data/*.fastq
+/test_data/*
 /workflow/.nextflow/*
 /workflow/work/*
 /workflow/output/*
+/.nextflow/*
+/data/*
+/work/*
+/output/*
 pipeline_trace*.txt*
 .nextflow*.log*
-report.html*
+report*.html*
 timeline*.html*
 
 *~

workflow/conf/biohpc.config

 process {
   executor = 'slurm'
   queue='super'
-
-  // Process specific configuration
-  $checkDesignFile {
-    module = ['python/3.6.1-2-anaconda']
-    executor = 'local'
-  }
-  $count2 {
-    module = ['cellranger/2.1.1']
-  }
-  $count3 {
-    module = ['cellranger/3.0.1']
-  }
 }
 
 trace {

workflow/main.nf

@@ -8,7 +8,7 @@ params.run = "TRUE"
 
 process copy {
 
-  publishDir "$baseDir/output/", mode: 'copy'
+  publishDir "$baseDir/output/", mode: 'symlink'
 
   input:
 
@@ -22,6 +22,6 @@ process copy {
   script:
 
   """
-  cp -r /project/shared/bicf_workflow_ref/tcga_shiny_app_data/* .
+  ln -s /project/shared/bicf_workflow_ref/tcga_shiny_app_data/* .
   """
 }