added Channel for pbccs input files and added mapping process

nextflow/backmap.nf

@@ -226,23 +226,27 @@ final Map<String, String> LOGFILES = [path: output, mode: 'copy', pattern: '*.{l
 */
 
 if (bamAvailable) {
-    chIlluminaBamMerge = (illuminaBamsAvailable) ? Channel.from(illuminaBamFiles)
+    chIlluminaBamMerge  = (illuminaBamsAvailable ) ? Channel.from(illuminaBamFiles )
         .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) } : Channel.empty()
-    chPacbioBamMerge   = (pacbioBamsAvailable)   ? Channel.from(pacbioBamFiles  )
+    chPacbioBamMerge    = (pacbioBamsAvailable   ) ? Channel.from(pacbioBamFiles   )
         .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) } : Channel.empty()
-    chNanoporeBamMerge = (nanoporeBamsAvailable) ? Channel.from(nanoporeBamFiles)
+    chPacbioCCSBamMerge = (pacbioCCSBamsAvailable) ? Channel.from(pacbioCCSBamFiles)
+        .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) } : Channel.empty()
+    chNanoporeBamMerge  = (nanoporeBamsAvailable ) ? Channel.from(nanoporeBamFiles )
         .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) } : Channel.empty()
 } else if (assemblyAvailable) { //fi: bamAvailable
     chAssembly            = Channel.fromPath(assembly).first()
     chBwaIndexGenome      = (pairedAvailable || unpairedAvailable) ? Channel.fromPath(assembly) : Channel.empty()
 
-    chUnpairedReadMapping = (unpairedAvailable) ? Channel.from(singleEnd)
+    chUnpairedReadMapping  = (unpairedAvailable ) ? Channel.from(singleEnd)
         .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) }.collate(1) : Channel.empty()
-    chPairedReadMapping   = (pairedAvailable  ) ? Channel.from(pairedEnd)
+    chPairedReadMapping    = (pairedAvailable   ) ? Channel.from(pairedEnd)
         .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) }.collate(2) : Channel.empty()
-    chPacbioReadMapping   = (pacbioAvailable  ) ? Channel.from(pacbio   )
+    chPacbioReadMapping    = (pacbioAvailable   ) ? Channel.from(pacbio   )
+        .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) }.collate(1) : Channel.empty()
+    chPacbioCCSReadMapping = (pacbioCCSAvailable) ? Channel.from(pacbioCCS)
         .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) }.collate(1) : Channel.empty()
-    chNanoporeReadMapping = (nanoporeAvailable) ? Channel.from(nanopore )
+    chNanoporeReadMapping  = (nanoporeAvailable ) ? Channel.from(nanopore )
         .map { files -> files.split(fileSeparator) }.flatten().map { f -> file(f) }.collate(1) : Channel.empty()
 
     // Create index files for bwa mapping
@@ -313,6 +317,23 @@ if (bamAvailable) {
             """
     } // process pacbioMapping
 
+    // Minimap2 mapping with PacBio CCS reads
+    process pacbioCCSMapping {
+        publishDir COPYMODETMP
+        cpus { PROCESSMAXTHREADS > threads ? threads : PROCESSMAXTHREADS }
+        input:
+            file pb from chPacbioCCSReadMapping
+            file gen from chAssembly
+        output:
+            file "${prefix}.pb_ccs${task.index}.bam" into chPacbioCCSBamMerge
+            file '*.err' into chPacbioCCSMappingLog
+        script:
+            """
+            minimap2 $minimapPacbioCCSOptions -x asm20 -a -t ${task.cpus} $gen $pb 2> \
+            ${prefix}_minimap_pb${task.index}.err | samtools view -1 -b - > ${prefix}.pb${task.index}.bam
+            """
+    } // process pacbioCCSMapping
+
     // Minimap2 mapping with Nanopore reads
     process nanoporeMapping {
         publishDir COPYMODETMP