feat: remove read_group which should be set up with task.ext.args (#1521)

* feat: remove reat_group which should be set up with ext.args

* fix: simplify dragmap command

modules/bwa/mem/main.nf

@@ -23,14 +23,12 @@ process BWA_MEM {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
 
     bwa mem \\
         $args \\
-        $read_group \\
         -t $task.cpus \\
         \$INDEX \\
         $reads \\

modules/bwamem2/mem/main.nf

@@ -23,7 +23,6 @@ process BWAMEM2_MEM {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
@@ -31,7 +30,6 @@ process BWAMEM2_MEM {
     bwa-mem2 \\
         mem \\
         $args \\
-        $read_group \\
         -t $task.cpus \\
         \$INDEX \\
         $reads \\

modules/dragmap/align/main.nf

@@ -24,44 +24,23 @@ process DRAGMAP_ALIGN {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def read_group = meta.read_group ? "--RGSM ${meta.read_group}" : ""
+    def reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
     def samtools_command = sort_bam ? 'sort' : 'view'
-    if (meta.single_end) {
-        """
-        dragen-os \\
-            -r $hashmap \\
-            $args \\
-            $read_group \\
-            --num-threads $task.cpus \\
-            -1 $reads \\
-            2> ${prefix}.dragmap.log \\
-            | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            dragmap: \$(echo \$(dragen-os --version 2>&1))
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
-        """
-    } else {
-        """
-        dragen-os \\
-            -r $hashmap \\
-            $args \\
-            $read_group \\
-            --num-threads $task.cpus \\
-            -1 ${reads[0]} \\
-            -2 ${reads[1]} \\
-            2> ${prefix}.dragmap.log \\
-            | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
+    """
+    dragen-os \\
+        -r $hashmap \\
+        $args \\
+        --num-threads $task.cpus \\
+        $reads_command \\
+        2> ${prefix}.dragmap.log \\
+        | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            dragmap: \$(echo \$(dragen-os --version 2>&1))
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
-        """
-    }
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dragmap: \$(echo \$(dragen-os --version 2>&1))
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
 }