create hpc-modules profile

env/bases2fastq/Dockerfile

@@ -0,0 +1,2 @@
+FROM elembio/bases2fastq:2.1.0
+CMD ["bases2fastq "]

env/picard/Dockerfile

@@ -0,0 +1,2 @@
+FROM broadinstitute/picard:2.3
+CMD ["/bin/bash"]

launch.sh

@@ -10,6 +10,7 @@
 
 module purge
 module load nextflow/23.04.1
+module load mambaforge/23.1.0
 
 run_dir_path=$1
 fcid=$2

main.nf

@@ -77,8 +77,6 @@ process tar {
 
 	tag "${fcid}"
 
-  module params.PBZIP2_MODULE
-
 	output:
 	path("*.tar.bz2"), emit: file
 	path(".command.*")
@@ -122,8 +120,6 @@ process _basecall_bases2fastq {
 
   tag "${fcid}"
 
-  module params.BASES2FASTQ_MODULE
-
   input:
   val lane
 
@@ -194,9 +190,6 @@ process _basecall_picard{
 
   tag "${fcid}"
 
-  module params.PICARD_MODULE
-  module params.JDK_MODULE
-
   input:
   val lane
 
@@ -475,8 +468,6 @@ process multiqc {
 
     tag "${fcid}"
 
-    module params.MULTIQC_MODULE
-
     input:
     tuple(val(path_to_data), path(fastqc))
     path reports

nextflow.config.template → nextflow.config

@@ -118,3 +118,61 @@ trace {
 env {
   SEQERA_ACCESS_TOKEN=""
 }
+
+profiles {
+    hpc-modules {
+        process {
+            withName: 'multiqc' {
+                module = params.MULTIQC_MODULE
+            }  
+            withName: 'tar' {
+                module = params.PBZIP2_MODULE
+            } 
+            withName: '_basecall_bases2fastq' {
+                module = params.BASES2FASTQ_MODULE
+            }
+            withName: '_basecall_picard' {
+                module = params.PICARD_MODULE
+                module = params.JDK_MODULE
+            }
+        }
+    }
+
+    hpc-container {
+        singularity.enabled = true
+
+        process {
+            container = /path/to/conda-container
+
+            withName: '_basecall_picard' {
+                container = 'docker://broadinstitute/picard:2.23.8'
+            }
+
+            withName: 'bases2fastq' {
+                container = 'docker://elembio/bases2fastq:2.2.0'
+            }
+        }
+    }
+
+    default {
+        singularity.enabled = true
+
+        conda.enabled = true
+        #conda.cacheDir = 
+        #conda.useMamba = true
+
+
+        process {
+            conda = ${baseDir}/environment.yml
+
+            withName: '_basecall_picard' {
+                container = 'docker://broadinstitute/picard:2.3'
+            }
+
+            withName: 'bases2fastq' {
+                container = 'docker://elembio/bases2fastq:2.1.0'
+            }
+
+        }
+    }
+}