Merge branch 'dev' into dsl2-genotyping

nf-core · Mar 19, 2024 · d39a10a · d39a10a
2 parents ccd118c + 43dce8f
commit d39a10a
Showing 1 changed file with 25 additions and 15 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -407,7 +407,11 @@ process {
 
     withName: 'BWA_SAMSE|BWA_SAMPE' {
         tag = { "${meta.id_index}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
-        ext.args = { "-r '@RG\\tID:ILLUMINA-${meta.library_id}\\tSM:${meta.sample_id}\\tPL:illumina\\tPU:ILLUMINA-${meta.library_id}-${meta.strandedness}'" }
+        ext.args = {
+            se_pe_string = meta.single_end ? "SE" : "PE"
+            [
+                "-r '@RG\\tID:ILLUMINA-${meta.sample_id}_${meta.library_id}\\tSM:${meta.sample_id}\\tLB:${meta.library_id}\\tPL:illumina\\tPU:ILLUMINA-${meta.library_id}-${meta.strandedness}_stranded-${se_pe_string}'"
+            ].join(' ').trim() }
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
         publishDir = [
             enabled: false
@@ -435,10 +439,12 @@ process {
 
     withName: BWA_MEM {
         tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
-        ext.args = {[
-            "-k ${params.mapping_bwamem_k}",
-            "-r ${params.mapping_bwamem_r}",
-            "-R '@RG\\tID:ILLUMINA-${meta.library_id}\\tSM:${meta.sample_id}\\tPL:illumina\\tPU:ILLUMINA-${meta.library_id}-${meta.strandedness}'"
+        ext.args = {
+            se_pe_string = meta.single_end ? "SE" : "PE"
+            [
+                "-k ${params.mapping_bwamem_k}",
+                "-r ${params.mapping_bwamem_r}",
+                "-R '@RG\\tID:ILLUMINA-${meta.sample_id}_${meta.library_id}\\tSM:${meta.sample_id}\\tLB:${meta.library_id}\\tPL:illumina\\tPU:ILLUMINA-${meta.library_id}-${meta.strandedness}_stranded-${se_pe_string}'"
             ].join(' ').trim() }
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
         publishDir = [
@@ -448,16 +454,20 @@ process {
 
     withName: BOWTIE2_ALIGN {
         tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
-        ext.args = {[ "-N ${params.mapping_bowtie2_n}",
-            "-L ${params.mapping_bowtie2_l}",
-            "--trim5 ${params.mapping_bowtie2_trim5}",
-            "--trim3 ${params.mapping_bowtie2_trim3}",
-            "--maxins ${params.mapping_bowtie2_maxins}",
-            "--rg-id ILLUMINA-${meta.library_id}",
-            "--rg SM:${meta.sample_id}",
-            "--rg PL:illumina",
-            "--rg PU:ILLUMINA-${meta.library_id}-${meta.strandedness}",
-            "${params.mapping_bowtie2_alignmode}" == 'local' ? "--local --${params.mapping_bowtie2_sensitivity}-local" : ( "${params.mapping_bowtie2_alignmode}" == 'end-to-end' ? "--end-to-end --${params.mapping_bowtie2_sensitivity}" : "" )
+        ext.args = {
+            se_pe_string = meta.single_end ? "SE" : "PE"
+            [
+                "-N ${params.mapping_bowtie2_n}",
+                "-L ${params.mapping_bowtie2_l}",
+                "--trim5 ${params.mapping_bowtie2_trim5}",
+                "--trim3 ${params.mapping_bowtie2_trim3}",
+                "--maxins ${params.mapping_bowtie2_maxins}",
+                "--rg-id ILLUMINA-${meta.library_id}",
+                "--rg SM:${meta.sample_id}",
+                "--rg LB:${meta.library_id}",
+                "--rg PL:illumina",
+                "--rg PU:ILLUMINA-${meta.sample_id}_${meta.library_id}-${meta.strandedness}_stranded-${se_pe_string}",
+                "${params.mapping_bowtie2_alignmode}" == 'local' ? "--local --${params.mapping_bowtie2_sensitivity}-local" : ( "${params.mapping_bowtie2_alignmode}" == 'end-to-end' ? "--end-to-end --${params.mapping_bowtie2_sensitivity}" : "" )
         ].join(' ').trim()}
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
         publishDir = [