From 2c25a7312044d637f71f9b6be00eea7ec54da359 Mon Sep 17 00:00:00 2001
From: MartinPippel <martin.pippel@nbis.se>
Date: Thu, 21 Nov 2024 12:36:50 +0100
Subject: [PATCH] cleanup, remove -5 bwa default argument, remove samtools
 fixmate step, add ugly grep hack to avoid samtools header issue

---
 configs/modules.config                                   | 9 ++++-----
 .../local/hic_curation/tworeadcombiner_fixmate_sort.nf   | 2 +-
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/configs/modules.config b/configs/modules.config
index a224035..c63b04a 100644
--- a/configs/modules.config
+++ b/configs/modules.config
@@ -319,9 +319,9 @@ process {
     }
 
     // scaffolding
-    withName: 'BWAMEM2_MEM' {
+    withName: 'BWAMEM2_MEM_SCAFFOLD' {
         ext.prefix = { "${meta.id}_${meta.assembly.build}_${reads.head().getBaseName(reads.head().name.endsWith(".gz") ? 2 : 1)}" }
-        ext.args   = '-5SP -T0'
+        ext.args   = '-SP -T0'
         ext.args2  = { sort_bam ? "--write-index" : "" }
     }
 
@@ -371,7 +371,7 @@ process {
     // scaffolding curation
     withName: 'BWAMEM2_MEM_CURATION' {
         ext.prefix = { "${meta.id}_${meta.assembly.build}_${reads.head().getBaseName(reads.head().name.endsWith(".gz") ? 2 : 1)}" }
-        ext.args   = '-5SP -T0'
+        ext.args   = '-SP -T0'
         ext.args2  = { sort_bam ? "--write-index" : "" }
     }
 
@@ -382,8 +382,7 @@ process {
     withName: 'TWOREADCOMBINER_FIXMATE_SORT' {
         ext.prefix = { "${bam.head().getBaseName(1)}" }
         ext.args   = { "${params.hic_map_qv}" }  // min hic map quality
-        ext.args2  = { "-mpu" }
-        ext.args3  = '--write-index -l1'
+        ext.args2  = '--write-index -l1'
     }
 
     withName: 'SCAFFOLD_CURATION:SAMTOOLS_MERGE_(HIFI|HIC)' {
diff --git a/modules/local/hic_curation/tworeadcombiner_fixmate_sort.nf b/modules/local/hic_curation/tworeadcombiner_fixmate_sort.nf
index 199099d..1b34dbe 100644
--- a/modules/local/hic_curation/tworeadcombiner_fixmate_sort.nf
+++ b/modules/local/hic_curation/tworeadcombiner_fixmate_sort.nf
@@ -22,7 +22,7 @@ process TWOREADCOMBINER_FIXMATE_SORT {
 
     """
     perl ${projectDir}/bin/two_read_bam_combiner_sanger.pl ${bam} samtools ${args} | \\
-    samtools fixmate -@${task.cpus} ${args2} - - | \\
+    grep -v -e "^@HD" | \\
     samtools sort ${args3} -@${task.cpus} -T sort_tmp -o ${prefix}_comb.bam -
 
     cat <<-END_VERSIONS > versions.yml