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

…, add ugly grep hack to avoid samtools header issue
NBISweden · Nov 21, 2024 · eab8bde · eab8bde
1 parent 2fca1ac
commit eab8bde
Show file tree

Hide file tree

Showing 4 changed files with 20 additions and 22 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
@@ -16,13 +16,12 @@ process TWOREADCOMBINER_FIXMATE_SORT {
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
-    def args3 = task.ext.args3 ?: ''
+    def args2 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     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

diff --git a/nextflow.config b/nextflow.config
@@ -71,7 +71,7 @@ params {
     // define how to sort the HiC-maps: [ length, name, nosort ]
     hic_map_sort_by        = 'length'
     // define minimum map quality for HiC alignments 
-    hic_map_qv             = 1
+    hic_map_qv             = 0
     // pacbio hifi coverage cap for pretext and higlass coverage track, e.g. cap repeats at <hifi_coverage_cap>
     hifi_coverage_cap      = 100
     // telomer motif

diff --git a/subworkflows/local/scaffold/main.nf b/subworkflows/local/scaffold/main.nf
@@ -1,16 +1,16 @@
-include { constructAssemblyRecord } from "$projectDir/modules/local/functions"
-include { getPrimaryAssembly      } from "$projectDir/modules/local/functions"
-include { joinByMetaKeys          } from "$projectDir/modules/local/functions"
-include { combineByMetaKeys       } from "$projectDir/modules/local/functions"
-include { BWAMEM2_INDEX           } from "$projectDir/modules/nf-core/bwamem2/index/main"
-include { BWAMEM2_MEM             } from "$projectDir/modules/nf-core/bwamem2/mem/main"
-include { SAMTOOLS_FAIDX          } from "$projectDir/modules/nf-core/samtools/faidx/main"
-include { PAIRTOOLS_PARSE         } from "$projectDir/modules/nf-core/pairtools/parse/main"
-include { PAIRTOOLS_SORT          } from "$projectDir/modules/nf-core/pairtools/sort/main"
-include { PAIRTOOLS_MERGE         } from "$projectDir/modules/nf-core/pairtools/merge/main"
-include { PAIRTOOLS_DEDUP         } from "$projectDir/modules/nf-core/pairtools/dedup/main"
-include { PAIRTOOLS_SPLIT         } from "$projectDir/modules/nf-core/pairtools/split/main"
-include { YAHS                    } from "$projectDir/modules/nf-core/yahs/main.nf"
+include { constructAssemblyRecord                 } from "$projectDir/modules/local/functions"
+include { getPrimaryAssembly                      } from "$projectDir/modules/local/functions"
+include { joinByMetaKeys                          } from "$projectDir/modules/local/functions"
+include { combineByMetaKeys                       } from "$projectDir/modules/local/functions"
+include { BWAMEM2_INDEX as BWAMEM2_INDEX_SCAFFOLD } from "$projectDir/modules/nf-core/bwamem2/index/main"
+include { BWAMEM2_MEM as BWAMEM2_MEM_SCAFFOLD     } from "$projectDir/modules/nf-core/bwamem2/mem/main"
+include { SAMTOOLS_FAIDX                          } from "$projectDir/modules/nf-core/samtools/faidx/main"
+include { PAIRTOOLS_PARSE                         } from "$projectDir/modules/nf-core/pairtools/parse/main"
+include { PAIRTOOLS_SORT                          } from "$projectDir/modules/nf-core/pairtools/sort/main"
+include { PAIRTOOLS_MERGE                         } from "$projectDir/modules/nf-core/pairtools/merge/main"
+include { PAIRTOOLS_DEDUP                         } from "$projectDir/modules/nf-core/pairtools/dedup/main"
+include { PAIRTOOLS_SPLIT                         } from "$projectDir/modules/nf-core/pairtools/split/main"
+include { YAHS                                    } from "$projectDir/modules/nf-core/yahs/main.nf"
 
 
 workflow SCAFFOLD {