add support pod5

add sumner2 node support

modules/UNTAR.nf

@@ -39,8 +39,8 @@ process UNTAR {
 			### deal with tar.gz
 			tar -xzf !{fast5Input} -C untarTempDir
 		elif [[ -d !{fast5Input} ]]; then
-			## Copy files, do not change original files such as old analyses data
-			find !{fast5Input}/ -name '*.fast5' | \
+			## For dir, should copy files, we do not want to change original files such as old analyses data in fast5
+			find !{fast5Input}/ \\( -name "*.fast5" -o -name "*.pod5" \\)  | \
 				parallel -j!{cores}  cp -L -f {} untarTempDir/
 		else
 			echo "### Untar error for input=!{fast5Input}"

nextflow.config

@@ -441,6 +441,55 @@ profiles {
 		}
 	}
 
+	sumner2 {
+		params{
+			max_cpus = 72
+			max_memory = 768.GB
+
+			gpu_queue = 'gpus' // winter only have one partition
+			gpu_qos = 'gpu_training' // or use training, time can be 14 days
+			gpu_processors = 8
+			gpu_memory = '128GB'
+			gpu_time = '14.d'
+			gpu_gresOptions = 'gpu:1' // null/false if no gpu needed
+
+			cpu_queue = 'compute' // winter only have one partition
+			cpu_qos = 'long' // or use training, time can be 14 days
+			cpu_processors = 8
+			cpu_memory = '128GB'
+			cpu_time = '14.d'
+
+			queueSize = 24
+		}
+
+		process{
+			executor = "slurm"
+			module = "slurm:singularity"
+
+			withName: 'UNTAR|ALIGNMENT|QCEXPORT|RESQUIGGLE|NANOPOLISH|Tombo|Guppy6Comb|METEORE|CLAIR3|PHASING|CONSENSUS|EVAL|REPORT|NPLSHCOMB|MGLDNCOMB|DPSIGCOMB|DEEPSIGNAL2COMB|GuppyComb|TomboComb|DpmodComb|Guppy6Comb' {
+				queue = params.cpu_queue
+				cpus = params.cpu_processors
+				memory = params.cpu_memory
+				time = params.cpu_time
+				clusterOptions = "-q ${params.cpu_qos}"
+			}
+
+			withName: 'ENVCHECK|BASECALL|MEGALODON|Guppy6|Guppy|DEEPSIGNAL|DEEPSIGNAL2|DeepMod|METEORE' {
+				queue = params.gpu_queue
+				cpus = params.gpu_processors
+				memory = params.gpu_memory
+				time = params.gpu_time
+				clusterOptions = "-q ${params.gpu_qos}  ${params.gpu_gresOptions  ? '--gres=' + params.gpu_gresOptions : '  '}"
+			}
+
+
+		}
+
+		executor {
+			queueSize = params.queueSize
+		}
+	}
+
 	// Google cloud computing platform
 	// ref doc: https://www.nextflow.io/docs/latest/google.html
 	// ref doc: https://www.nextflow.io/docs/latest/google.html#configuration