From c0e43f4df66d6c8a743dcd52177bc66bf152c095 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Mon, 18 Mar 2024 11:13:32 +0100
Subject: [PATCH 1/3] add LB and seqType to RGs. Update ID field to include
 sample id

---
 conf/modules.config | 40 +++++++++++++++++++++++++---------------
 1 file changed, 25 insertions(+), 15 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 6af54e23a..a9e0307f4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -403,7 +403,11 @@ 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
@@ -431,10 +435,12 @@ 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 = [
@@ -444,16 +450,20 @@ 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 = [

From 4628ba296348983cbdaaf57908eff9f77e3a2370 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Mon, 18 Mar 2024 11:17:11 +0100
Subject: [PATCH 2/3] random commit to restart CI

---
 conf/modules.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/modules.config b/conf/modules.config
index a9e0307f4..a5f6ba23d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -401,6 +401,7 @@ process {
         ]
     }
 
+
     withName: 'BWA_SAMSE|BWA_SAMPE' {
         tag = { "${meta.id_index}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         ext.args = {

From 33e858b6e990924d5a8f421addc4df9c107875e3 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Mon, 18 Mar 2024 11:17:20 +0100
Subject: [PATCH 3/3] Revert "random commit to restart CI"

This reverts commit 4628ba296348983cbdaaf57908eff9f77e3a2370.
---
 conf/modules.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index a5f6ba23d..a9e0307f4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -401,7 +401,6 @@ process {
         ]
     }
 
-
     withName: 'BWA_SAMSE|BWA_SAMPE' {
         tag = { "${meta.id_index}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         ext.args = {