DSL2: Add mapAD

.github/workflows/ci.yml

@@ -48,6 +48,7 @@ jobs:
           - " --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
           - " --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
           - " --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
+          - " --mapping_tool mapad"
           - " --mapping_tool circularmapper --skip_preprocessing --convert_inputbam --fasta_circular_target 'NC_007596.2' --fasta_circularmapper_elongationfactor 500"
           - "_humanbam --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
           - "_humanbam --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"

README.md

@@ -30,7 +30,7 @@
 - (Optionally) create reference genome indices for mapping (`bwa`, `samtools`, and `picard`)
 - Sequencing quality control (`FastQC`, `Falco`)
 - Sequencing adapter removal, paired-end data merging (`AdapterRemoval`)
-- Read mapping to reference using (`bwa aln`, `bwa mem`, `CircularMapper`, or `bowtie2`)
+- Read mapping to reference using (`bwa aln`, `bwa mem`, `CircularMapper`, `bowtie2`, or `mapAD`)
 - Post-mapping processing, statistics and conversion to bam (`samtools`, and `preseq`)
 - Ancient DNA C-to-T damage pattern visualisation (`DamageProfiler`)
 - PCR duplicate removal (`DeDup` or `MarkDuplicates`)

conf/modules.config

@@ -358,6 +358,15 @@ process {
         ]
     }
 
+    withName: MAPAD_INDEX {
+        publishDir = [
+            path: { "${params.outdir}/reference/${meta.id}/" },
+            mode: params.publish_dir_mode,
+            pattern: 'mapad',
+            enabled: params.save_reference
+        ]
+    }
+
     //
     // BAM INPUT
     //
@@ -602,7 +611,32 @@ process {
         ]
     }
 
-    withName: 'SAMTOOLS_INDEX_MEM|SAMTOOLS_INDEX_BT2' {
+    withName: MAPAD_MAP {
+        tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
+        ext.args = {
+            [
+                "-x ${params.mapping_mapad_x}",
+                "--gap_dist_ends ${params.mapping_mapad_gapreadenddistance}",
+                "--max_num_gaps_open ${params.mapping_mapad_maxnumopengaps}",
+                "-D ${params.mapping_mapad_baseerrorrate}",
+                params.mapping_mapad_ignorebasequal ? "--ignore_base_quality" : "",
+                params.mapping_mapad_stacklimitabort ? "--stack_limit_abort" : "",
+            ].join(' ').trim()}
+        ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}_unsorted" }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: "SAMTOOLS_SORT_MAPAD" {
+        tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
+        ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: 'SAMTOOLS_INDEX_MEM|SAMTOOLS_INDEX_BT2|SAMTOOLS_INDEX_MAPAD' {
         tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         ext.args = { params.fasta_largeref ? "-c" : "" }
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }

modules.json

@@ -200,6 +200,16 @@
                         "git_sha": "8840ece9ee7528480dec95796e017be02ada0dc0",
                         "installed_by": ["modules"]
                     },
+                    "mapad/index": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["modules"]
+                    },
+                    "mapad/map": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["modules"]
+                    },
                     "mapdamage2": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",

nextflow.config

@@ -119,6 +119,18 @@ params {
     mapping_bowtie2_trim3                 = 0
     mapping_bowtie2_maxins                = 500
     mapping_circularmapper_circularfilter = false
+    mapping_mapad_p                       = 0.03
+    mapping_mapad_f                       = 0.5
+    mapping_mapad_t                       = 0.5
+    mapping_mapad_d                       = 0.02
+    mapping_mapad_s                       = 1.0
+    mapping_mapad_i                       = 0.001
+    mapping_mapad_x                       = 0.5
+    mapping_mapad_gapreadenddistance      = 5
+    mapping_mapad_maxnumopengaps          = 2
+    mapping_mapad_baseerrorrate           = 0.02
+    mapping_mapad_ignorebasequal          = false
+    mapping_mapad_nosearchlimitrecovery   = false
 
     // BAM Filtering
     run_bamfiltering                      = false