Fix configs and refs

workflow/configs/aws.config

@@ -12,27 +12,27 @@ process {
   cpus = 1
   memory = '1 GB'
 
-  withLabel: checkDesignFile {
+  withName: checkDesignFile {
     cpus = 2
     memory = '1 GB'
   }
-  withLabel: count211 {
+  withName: count211 {
     cpus = 2
     memory = '30 GB'
   }
-  withLabel: count302 {
+  withName: count302 {
     cpus = 2
     memory = '30 GB'
   }
-  withLabel: count310 {
+  withName: count310 {
     cpus = 2
     memory = '30 GB'
   }
-  withLabel: versions {
+  withName: versions {
     cpus = 3
     memory = '1 GB'
   }
-  withLabel: multiqc {
+  withName: multiqc {
     cpus = 1
     memory = '1 GB'
   }

workflow/configs/cluster.config

@@ -9,25 +9,25 @@ process {
   withLabel: checkDesignFile {
     executor = 'local'
   }
-  withLabel: count211 {
+  withName: count211 {
     queue = '128GB,256GB,256GBv1,384GB'
   }
-  withLabel: count220 {
+  withName: count220 {
     queue = '128GB,256GB,256GBv1,384GB'
   }
-  withLabel: count302 {
+  withName: count302 {
     queue = '128GB,256GB,256GBv1,384GB'
   }
-  withLabel: count310 {
+  withName: count310 {
     queue = '128GB,256GB,256GBv1,384GB'
   }
-  withLabel: count400 {
+  withName: count400 {
     queue = '128GB,256GB,256GBv1,384GB'
   }
-  withLabel: versions {
+  withName: versions {
     executor = 'local'
   }
-  withLabel: multiqc {
+  withName: multiqc {
     executor = 'local'
   }
 }

workflow/main.nf

@@ -22,7 +22,6 @@ params.name = "run"
 params.fastq = "test_data/mu.v3s1r500/*.fastq.gz"
 params.designFile = "test_data/mu.v3s1r500/design.csv"
 params.genome = 'mm10-2020-A'
-params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-'
 params.expectCells = 10000
 params.forceCells = 0
 params.kitVersion = '3GEXv3'
@@ -39,7 +38,11 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
 // Define variables if astrocyte (or from config)
 if (params.astrocyte) {
   print("Running under astrocyte")
-  params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
+  if (params.version == "4.0.0") {
+    params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-'
+  } else {
+    params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
+  }
   if (params.kitVersion == "3GEXv1") {
     params.chemistryParam ='SC3Pv1'
   } else if (params.kitVersion == "3GEXv2") {

workflow/nextflow.config

 profiles {
   standard {
     includeConfig 'configs/biohpc.config'
+    includeConfig 'configs/cluster.config'
   }
   biohpc {
     includeConfig 'configs/biohpc.config'