feat: update dragmap to follow new bwa/mem + bwamem2/mem logic (#1146)

modules/dragmap/align/main.nf

@@ -10,6 +10,7 @@ process DRAGMAP_ALIGN {
     input:
     tuple val(meta), path(reads)
     path  hashmap
+    val   sort_bam
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -20,6 +21,7 @@ process DRAGMAP_ALIGN {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def samtools_command = sort_bam ? 'sort' : 'view'
     if (meta.single_end) {
         """
         dragen-os \\
@@ -28,7 +30,7 @@ process DRAGMAP_ALIGN {
             --num-threads $task.cpus \\
             $args \\
             2> ${prefix}.dragmap.log \\
-            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
+            | samtools $samtools_command -@ $task.cpus $args2 -o ${prefix}.bam -
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -46,7 +48,7 @@ process DRAGMAP_ALIGN {
             --num-threads $task.cpus \\
             $args \\
             2> ${prefix}.dragmap.log \\
-            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
+            | samtools $samtools_command -@ $task.cpus $args2 -o ${prefix}.bam -
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":

tests/modules/dragmap/align/main.nf

@@ -3,7 +3,7 @@
 nextflow.enable.dsl = 2
 
 include { DRAGMAP_HASHTABLE } from '../../../../modules/dragmap/hashtable/main.nf'
-include { DRAGMAP_ALIGN } from '../../../../modules/dragmap/align/main.nf'
+include { DRAGMAP_ALIGN     } from '../../../../modules/dragmap/align/main.nf'
 
 workflow test_dragmap_align_single_end {
     input = [
@@ -15,7 +15,20 @@ workflow test_dragmap_align_single_end {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     DRAGMAP_HASHTABLE ( fasta )
-    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
+}
+
+workflow test_dragmap_align_single_end_sort {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    DRAGMAP_HASHTABLE ( fasta )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
 }
 
 workflow test_dragmap_align_paired_end {
@@ -29,5 +42,19 @@ workflow test_dragmap_align_paired_end {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     DRAGMAP_HASHTABLE ( fasta )
-    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
+}
+
+workflow test_dragmap_align_paired_end_sort {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    DRAGMAP_HASHTABLE ( fasta )
+    DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
 }

tests/modules/dragmap/align/nextflow.config

@@ -1,5 +1,9 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
+
-}
+    withName: DRAGMAP_ALIGN {
+        ext.args2 = { sort_bam ? "" : "-bh" }
+    }
+
+}

tests/modules/dragmap/align/test.yml

@@ -7,6 +7,15 @@
     - path: output/dragmap/test.bam
     - path: output/dragmap/test.dragmap.log
 
+- name: dragmap align single-end_sort
+  command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_single_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config
+  tags:
+    - dragmap
+    - dragmap/align
+  files:
+    - path: output/dragmap/test.bam
+    - path: output/dragmap/test.dragmap.log
+
 - name: dragmap align paired-end
   command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config
   tags:
@@ -15,3 +24,12 @@
   files:
     - path: output/dragmap/test.bam
     - path: output/dragmap/test.dragmap.log
+
+- name: dragmap align paired-end_sort
+  command: nextflow run ./tests/modules/dragmap/align -entry test_dragmap_align_paired_end_sort -c ./tests/config/nextflow.config -c ./tests/modules/dragmap/align/nextflow.config
+  tags:
+    - dragmap
+    - dragmap/align
+  files:
+    - path: output/dragmap/test.bam
+    - path: output/dragmap/test.dragmap.log