Make bicfbase default container

workflow/conf/biohpc.config

@@ -2,13 +2,13 @@ process {
   executor = 'slurm'
   queue = 'super'
   clusterOptions = '--hold'
+  container = 'docker://bicf/bicfbase:1.3'
 
   withLabel:checkDesignFile {
     container = 'docker://bicf/python3:1.2'
     executor = 'local'
   }
   withLabel:untarBCL {
-    container = 'docker://bicf/bicfbase:1.3'
     queue = 'super'
   }
   withLabel:mkfastq {
@@ -16,7 +16,6 @@ process {
     queue = '128GB,256GB,256GBv1,384GB'
   }
   withLabel:countDesign {
-    container = 'docker://bicf/bicfbase:1.3'
     executor = 'local'
   }
   withLabel:fastqc {

workflow/conf/biohpc_local.config

 process {
   executor = 'local'
+  container = 'docker://bicf/bicfbase:1.3'
 
   withLabel:checkDesignFile {
     container = 'docker://bicf/python3:1.2'
   }
   withLabel:untarBCL {
-    container = 'docker://bicf/bicfbase:1.3'
   }
   withLabel:mkfastq {
     container = 'docker://bicf/cellranger3.1.0:1.0'
   }
   withLabel:countDesign {
-    container = 'docker://bicf/bicfbase:1.3'
   }
   withLabel:fastqc {
     module = ['fastqc/0.11.5', 'parallel']

workflow/nextflow.config

@@ -30,14 +30,14 @@ report {
 }
 
 tower {
-  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
   enabled = true
+  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
 }
 
 manifest {
-  homePage = 'https://https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
+  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 = 'v1.4.0_indev'
-  nextflowVersion = '>=19.09.0'
+  nextflowVersion = '>=0.31.0'
 }
\ No newline at end of file