Add mapAD indexing

Author: jch-13

subworkflows/local/map.nf

@@ -128,7 +128,7 @@ workflow MAP {
                 params.mapping_mapad_i
                 )
         ch_versions        = ch_versions.mix ( FASTQ_ALIGN_MAPAD.out.versions.first() )
-        ch_mapped_lane_bam = FASTQ_ALIGN_BWAALN.out.bam
+        ch_mapped_lane_bam = FASTQ_ALIGN_MAPAD.out.bam
                                 .map{
                                     // create meta consistent with rest of workflow
                                     meta, bam ->

subworkflows/local/reference_indexing_multi.nf

@@ -7,6 +7,7 @@ include { BWA_INDEX                       } from '../../modules/nf-core/bwa/inde
 include { BOWTIE2_BUILD                   } from '../../modules/nf-core/bowtie2/build/main'
 include { SAMTOOLS_FAIDX                  } from '../../modules/nf-core/samtools/faidx/main'
 include { PICARD_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/picard/createsequencedictionary/main'
+include { MAPAD_INDEX                     } from '../../modules/nf-core/mapad/index/main'
 // TODO missing: circulargeneraotr?
 
 workflow REFERENCE_INDEXING_MULTI {
@@ -188,6 +189,10 @@ workflow REFERENCE_INDEXING_MULTI {
         ch_indexed_forremap = BOWTIE2_BUILD.out.index
     } else if ( params.mapping_tool == "circularmapper" ) {
         println("CircularMapper Indexing Not Yet Implemented")
+    } else if ( params.mapping_tool == "mapad" ) {
+        MAPAD_INDEX ( ch_mapindex_input.index )
+        ch_version = ch_versions.mix( MAPAD_INDEX.out.versions )
+        ch_indexed_forremap = MAPAD_INDEX.out.index
     }
 
     ch_indexed_formix = ch_indexed_forremap

subworkflows/local/reference_indexing_single.nf

@@ -8,6 +8,7 @@ include { BWA_INDEX                       } from '../../modules/nf-core/bwa/inde
 include { BOWTIE2_BUILD                   } from '../../modules/nf-core/bowtie2/build/main'
 include { SAMTOOLS_FAIDX                  } from '../../modules/nf-core/samtools/faidx/main'
 include { PICARD_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/picard/createsequencedictionary/main'
+include { MAPAD_INDEX                     } from '../../modules/nf-core/mapad/index/main'
 // TODO missing: circulargeneraotr?
 
 workflow REFERENCE_INDEXING_SINGLE {
@@ -70,6 +71,14 @@ workflow REFERENCE_INDEXING_SINGLE {
             ch_fasta_mapperindexdir = Channel.fromPath(fasta_mapperindexdir).map{[[id: clean_name], it ]}
         }
 
+    } else if ( params.mapping_tool == "mapad" ) {
+
+        if ( !fasta_mapperindexdir ) {
+            ch_fasta_mapperindexdir = MAPAD_INDEX ( ch_ungz_ref ).index
+            ch_versions = ch_versions.mix( MAPAD_INDEX.out.versions.first())
+        } else {
+            ch_fasta_mapperindexdir = Channel.fromPath(fasta_mapperindexdir).map{[[id: clean_name], it ]}
+        }
     }
 
     // Join all together into a single map. failOnMismatch allows check if