PacBio HiFi specific reference alignment index added for Minimap2

jasmine-amir · jasmine-amir · commit c34646d79ab2 · 2023-07-08T17:13:38.000-04:00
diff --git a/covidRefSequences/PacBioHiFi.mmi b/covidRefSequences/PacBioHiFi.mmi
diff --git a/nextflow.config b/nextflow.config
@@ -60,9 +60,10 @@ process {
     }
 
     withName: 'freyjaVariantCaller' {
-        time = '2 h'
+        time = '3 h'
         maxForks = 20
         cpus = 15
+        // cpus = 20 
         memory = '24 GB'
     }
     
diff --git a/startWorkflow.nf b/startWorkflow.nf
@@ -152,7 +152,7 @@ process referenceAlignment {
                 minimap2 -a --sam-hit-only -2 -x map-ont ${refSeqBasename}.mmi R1.fastq.gz -t \$numThreads -o aligned.sam
                 ;;
             PacBio)
-                minimap2 -a --sam-hit-only -2 -x map-hifi ${refSeqBasename}.mmi R1.fastq.gz -t \$numThreads -o aligned.sam
+                minimap2 -a --sam-hit-only -2 -x map-hifi $projectDir/covidRefSequences/PacBioHiFi.mmi R1.fastq.gz -t \$numThreads -o aligned.sam
                 ;;
         esac
     """

Original file line number	Diff line number	Diff line change
`@@ -60,9 +60,10 @@ process {`
`60`	`60`	`}`
`61`	`61`
`62`	`62`	`withName: 'freyjaVariantCaller' {`
`63`		`- time = '2 h'`
	`63`	`+ time = '3 h'`
`64`	`64`	`maxForks = 20`
`65`	`65`	`cpus = 15`
	`66`	`+ // cpus = 20`
`66`	`67`	`memory = '24 GB'`
`67`	`68`	`}`
`68`	`69`