cleanup, remove -5 bwa default argument, remove samtools fixmate step…

…, add ugly grep hack to avoid samtools header issue
NBISweden · Nov 21, 2024 · 2c25a73 · 2c25a73
1 parent 2fca1ac
commit 2c25a73
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git 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
@@ -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