PacBio HiFi specific reference alignment index added for Minimap2

CFSAN-Biostatistics · Jul 8, 2023 · c34646d · c34646d
1 parent 9b39072
commit c34646d
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Showing 3 changed files with 3 additions and 2 deletions.
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 change
@@ Expand Up / @@ -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
         """
@@ Expand Down @@