usc config

README.md

@@ -339,11 +339,15 @@ Please check [NANOME report](https://github.com/LabShengLi/nanome/blob/master/do
 Please check [phasing usage](https://github.com/LabShengLi/nanome/blob/master/docs/Phasing.md).
 ![PhasingDemo](https://github.com/LabShengLi/nanome/blob/master/docs/resources/nanome3t_5mc_phasing2.png)
 
-### Lifebit CloudOS report
-We now support running NANOME on cloud computing platform. [Lifebit](https://lifebit.ai/lifebit-cloudos/) is a web-based cloud computing platform, and below is the running reports:
-* Ecoli test report: https://cloudos.lifebit.ai/public/jobs/6430509445941801546e5f8f
-* Human test report: https://cloudos.lifebit.ai/public/jobs/6430639045941801546e627f
-* NA12878 chr22 report: https://cloudos.lifebit.ai/public/jobs/6430b64645941801546e7400
+[//]: # (### Lifebit CloudOS report)
+
+[//]: # (We now support running NANOME on cloud computing platform. [Lifebit](https://lifebit.ai/lifebit-cloudos/) is a web-based cloud computing platform, and below is the running reports:)
+
+[//]: # (* Ecoli test report: https://cloudos.lifebit.ai/public/jobs/6430509445941801546e5f8f)
+
+[//]: # (* Human test report: https://cloudos.lifebit.ai/public/jobs/6430639045941801546e627f)
+
+[//]: # (* NA12878 chr22 report: https://cloudos.lifebit.ai/public/jobs/6430b64645941801546e7400)
 
 
 ## Revision History

conf/examples/test_dorado.config

@@ -1,10 +1,10 @@
 /*
  * -------------------------------------------------
- *  Nextflow config file for CI human test case
+ *  Nextflow config file for CI human test case for Dorado
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *    nextflow run LabShengLi/nanome -profile test,<docker/singularity>
+ *    nextflow run LabShengLi/nanome -profile test_dorado,<docker/singularity>
  */
 
 params{
@@ -28,7 +28,7 @@ process {
 	maxRetries = params.maxRetries
 
 	withName: 'ENVCHECK' {
-		// allow retry if download Rerio model failed
+		// allow retry if download files failed
 		errorStrategy = {task.attempt >= process.maxRetries ? params.errorStrategy :  'retry' }
 	}
 }

conf/executors/usc.config

@@ -0,0 +1,53 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow default input from USC CARC HPC
+ * -------------------------------------------------
+ * Defines bundled specific input data from USC CARC HPC
+ *
+ */
+params{
+	max_cpus = 16
+	max_memory = 128.GB
+
+	gpu_queue = 'gpu'
+	// gpu_qos = null
+	gpu_processors = 4
+	gpu_memory = '64.GB'
+	gpu_time = '2.d'
+	gpu_gresOptions = 'gpu:a100:1'
+
+	cpu_queue = 'main'
+	// cpu_qos = null
+	cpu_processors = 8
+	cpu_memory = '128.GB'
+	cpu_time = '2.d'
+
+	queueSize = 24
+	// used for singularity identify both file systems
+	containerOptions = '--nv -B /project/sli68423_1316 -B /scratch1/yliu8962'
+}
+
+process{
+	executor = "slurm"
+	// module = "slurm:singularity"
+	containerOptions = params.containerOptions
+
+	withName: 'ENVCHECK|UNTAR|ALIGNMENT|QCEXPORT|RESQUIGGLE|NANOPOLISH|Tombo|Guppy6Comb|METEORE|CLAIR3|PHASING|CONSENSUS|EVAL|REPORT|NPLSHCOMB|MGLDNCOMB|DPSIGCOMB|DEEPSIGNAL2COMB|GuppyComb|TomboComb|DpmodComb|Guppy6Comb|DORADO_DEMUX' {
+		queue = params.cpu_queue
+		cpus = params.cpu_processors
+		memory = params.cpu_memory
+		time = params.cpu_time
+	}
+
+	withName: 'BASECALL|MEGALODON|Guppy6|Guppy|DEEPSIGNAL|DEEPSIGNAL2|DeepMod|METEORE|DORADO_CALL' {
+		queue = params.gpu_queue
+		cpus = params.gpu_processors
+		memory = params.gpu_memory
+		time = params.gpu_time
+		clusterOptions = " ${params.gpu_gresOptions  ? '--gres=' + params.gpu_gresOptions : '  '}"
+	}
+}
+
+executor {
+	queueSize = params.queueSize
+}

main.nf

@@ -303,7 +303,7 @@ include { EVAL } from './modules/EVAL'
 
 include { REPORT } from './modules/REPORT'
 
-include { DORADO_UNTAR; DORADO_CALL; DORADO_QC; DORADO_CALL_EXTRACT; UNIFY } from './modules/DORADO'
+include { DORADO_UNTAR; DORADO_CALL; DORADO_DEMUX; DORADO_QC; DORADO_CALL_EXTRACT; UNIFY; CLAIR3_dorado } from './modules/DORADO'
 
 // place holder channel, used for empty file of a channel
 null1 = Channel.fromPath("${projectDir}/utils/null1")
@@ -333,23 +333,38 @@ workflow {
 	// environment check
 	ENVCHECK(ch_genome, ch_utils, ch_rerio_dir, ch_deepsignal_dir)
 
-
 	if (params.dorado) { // Dorado ecosystems
 		// ch_inputs.collect().view()
+		if (!params.input_bam) {
+			DORADO_UNTAR(ch_inputs.collect())
+			DORADO_CALL(DORADO_UNTAR.out.untar, ENVCHECK.out.reference_genome)
+			dorado_call = DORADO_CALL.out.dorado_call
+		} else {
+			dorado_call = ch_inputs.collect()
+		}
+
+		if (params.demux) {
+			DORADO_DEMUX(dorado_call)
+		} else { // demux will not run QC
+			DORADO_QC(dorado_call, ENVCHECK.out.reference_genome)
 
-		DORADO_UNTAR(ch_inputs.collect())
-		DORADO_CALL(DORADO_UNTAR.out.untar, ENVCHECK.out.reference_genome)
-		DORADO_QC(DORADO_CALL.out.dorado_call, ENVCHECK.out.reference_genome)
+			// bam_fn = "${params.dsname}.dorado_call/${params.dsname}.dorado_call.bam"
+			// extract per read
+			DORADO_CALL_EXTRACT("per_read",
+								dorado_call, ENVCHECK.out.reference_genome,
+								ch_src, ch_utils)
+
+			// convert to per site
+			UNIFY("Dorado","NANOME", "all",
+					DORADO_CALL_EXTRACT.out.dorado_call_extract,
+					ENVCHECK.out.reference_genome,
+					ch_src, ch_utils)
 
-		bam_fn = "${params.dsname}.dorado_call/${params.dsname}.dorado_call.bam"
-		DORADO_CALL_EXTRACT("per_read", bam_fn,
-							DORADO_CALL.out.dorado_call, ENVCHECK.out.reference_genome,
-							ch_src, ch_utils)
+			if (params.phasing) {
+				CLAIR3_dorado(dorado_call, ENVCHECK.out.reference_genome)
+			}
+		}
 
-		UNIFY("Dorado","NANOME", "all",
-				DORADO_CALL_EXTRACT.out.dorado_call_extract,
-				ENVCHECK.out.reference_genome,
-				ch_src, ch_utils)
 	} else { // Guppy ecosystems
 		if (params.runBasecall) {
 			UNTAR(ch_inputs)