Add dragmap aligner

conf/modules.config

@@ -52,6 +52,15 @@ process {
         ]
     }
 
+    withName: 'DRAGMAP_HASHTABLE' {
+        publishDir = [
+            path: { "${params.outdir}/reference/dragmap" },
+            enabled: "params.save_reference",
+            pattern: "dragmap"
+        ]
+
+    }
+
     withName: 'CREATE_INTERVALS_BED' {
         publishDir       = [
             enabled: "${params.save_reference}",
@@ -256,6 +265,13 @@ process {
         // Only name sort if Spark for Markduplicates + duplicate marking is not skipped
         ext.args2        = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.contains('markduplicates'))) ? '-n' : '' }
         ext.prefix       = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last()) : "" }
+
+    withName: "DRAGMAP_ALIGN" {
+        publishDir       = [ enabled: false ]
+        ext.prefix       = { params.split_fastq > 1 ? "${meta.id}".concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last().concat('.')) : "${meta.id}" }
+    }
+
+    withName: 'INDEX_MAPPING' {
         publishDir       = [
             enabled: false
         ]

docs/output.md

@@ -81,6 +81,12 @@ Such files are intermediate and not kept in the final files delivered to users.
 
 Such files are intermediate and not kept in the final files delivered to users.
 
+#### DRAGMAP
+
+[DRAGMAP](https://github.com/Illumina/dragmap) is an open-source software implementation of the DRAGEN mapper, which the Illumina team created so that we would have an open-source way to produce the same results as their proprietary DRAGEN hardware.
+
+Such files are intermediate and not kept in the final files delivered to users.
+
 ### Mark Duplicates
 
 #### GATK MarkDuplicates

modules.json

@@ -39,6 +39,12 @@
             "deepvariant": {
                 "git_sha": "c450b08a75cda8878876ccbbe42493d6774397bd"
             },
+            "dragmap/align": {
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
+            "dragmap/hashtable": {
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
             "ensemblvep": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },

nextflow_schema.json

@@ -204,10 +204,11 @@
                     "fa_icon": "fas fa-puzzle-piece",
                     "enum": [
                         "bwa-mem",
-                        "bwa-mem2"
+                        "bwa-mem2",
+                        "dragmap"
                     ],
                     "description": "Specify aligner to be used to map reads to reference genome.",
-                    "help_text": "> **WARNING** Current indices for `bwa` in AWS iGenomes are not compatible with `bwa-mem2`.\n> Use `--bwa=false` to have `Sarek` build them automatically.\n\n> **WARNING** BWA-mem2 is in active development\n> Sarek might not be able to require the right amount of resources for it at the moment\n> We recommend to use pre-built indexes",
+                    "help_text": "> **WARNING** Current indices for `bwa` in AWS iGenomes are not compatible with `bwa-mem2` and `dragmap`.\n> Use `--bwa=false` to have `Sarek` build them automatically.\n\n> **WARNING** BWA-mem2 is in active development\n> Sarek might not be able to require the right amount of resources for it at the moment\n> We recommend to use pre-built indexes",
                     "hidden": true
                 },
                 "markdup_java_options": {

subworkflows/local/prepare_genome.nf

@@ -10,6 +10,8 @@
 
 include { BWA_INDEX as BWAMEM1_INDEX             } from '../../modules/nf-core/modules/bwa/index/main'
 include { BWAMEM2_INDEX                          } from '../../modules/nf-core/modules/bwamem2/index/main'
+include { DRAGMAP_HASHTABLE                      } from '../../modules/nf-core/modules/dragmap/hashtable/main'
+include { CREATE_INTERVALS_BED                   } from '../../modules/local/create_intervals_bed/main'
 include { GATK4_CREATESEQUENCEDICTIONARY         } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main'
 include { MSISENSORPRO_SCAN                      } from '../../modules/nf-core/modules/msisensorpro/scan/main'
 include { SAMTOOLS_FAIDX                         } from '../../modules/nf-core/modules/samtools/faidx/main'
@@ -33,8 +35,11 @@ workflow PREPARE_GENOME {
 
     BWAMEM1_INDEX(fasta) // If aligner is bwa-mem
     BWAMEM2_INDEX(fasta) // If aligner is bwa-mem2
+    DRAGMAP_HASHTABLE(fasta)
     // if we use mix here, bwa becomes a channel that is comsumed
-    ch_bwa = params.aligner == "bwa-mem" ? BWAMEM1_INDEX.out.index : BWAMEM2_INDEX.out.index
+    ch_bwa = params.aligner == "bwa-mem" ?
+        BWAMEM1_INDEX.out.index : params.aligner == "dragmap" ?
+        DRAGMAP_HASHTABLE.out.hashmap : BWAMEM2_INDEX.out.index
 
     GATK4_CREATESEQUENCEDICTIONARY(fasta)
     MSISENSORPRO_SCAN(fasta.map{ it -> [[id:it[0].baseName], it] })

tests/test_aligner.yml

@@ -22,3 +22,27 @@
     - path: results/reports/qualimap/test/test.recal
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
+- name: Run dragmap
+  command: nextflow run main.nf -profile test,docker --aligner dragmap
+  tags:
+    - aligner
+    - dragmap
+    - preprocessing
+  files:
+    - path: results/multiqc
+    - path: results/preprocessing/test/markduplicates/test.md.cram
+    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
+    - path: results/preprocessing/test/recal_table/test.recal.table
+    - path: results/preprocessing/test/recalibrated/test.recal.cram
+    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/csv/markduplicates.csv
+    - path: results/preprocessing/csv/markduplicates_test.csv
+    - path: results/preprocessing/csv/markduplicates_no_table.csv
+    - path: results/preprocessing/csv/markduplicates_no_table_test.csv
+    - path: results/preprocessing/csv/recalibrated.csv
+    - path: results/preprocessing/csv/recalibrated_test.csv
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/qualimap/test/test.mapped
+    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/samtools_stats/test/test.md.cram.stats
+    - path: results/reports/samtools_stats/test/test.recal.cram.stats