Patch modules

CHANGELOG.md

@@ -22,6 +22,7 @@ Initial release of Joon-Klaps/viralgenie, created with the [nf-core](https://nf-
 - Update docs ([#150](https://github.com/Joon-Klaps/viralgenie/pull/150))
 - Make custom-mpileup.py postion 1 index based and not 0 index to follow bcftools ([#153](https://github.com/Joon-Klaps/viralgenie/pull/153))
 - Update docs for more streamlined docs & figures ([#154](https://github.com/Joon-Klaps/viralgenie/pull/154))
+- Patch modules ([#159](https://github.com/Joon-Klaps/viralgenie/pull/159))
 
 ### `Fixed`
 

conf/modules.config

@@ -12,6 +12,7 @@
 
 variant_caller              = params.variant_caller
 intermediate_variant_caller = params.intermediate_variant_caller
+search_mode                 = params.mmseqs_searchtype
 assemblers                  = params.assemblers ? params.assemblers.split(',').collect{ it.trim().toLowerCase() } : []
 id_threshold_cdhit          = Math.max(params.identity_threshold > 1 ? params.identity_threshold * 0.01 : params.identity_threshold, 0.80)
 save_final_reads            = params.save_final_reads ? (!params.skip_hostremoval ? 'host' : (!params.skip_complexity_filtering ? 'complexity' : (!params.skip_humid ? 'deduplication' : 'trimming')))  : 'nothing'
@@ -1652,7 +1653,11 @@ process {
         }
 
         withName: MMSEQS_EASYSEARCH {
-            ext.args= { "--search-type ${params.mmseqs_searchtype} --rescore-mode 3 --format-output query,target,theader,fident,qlen,tlen,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits" } // don't change format-output
+            ext.args= [
+                mmseqs_searchtype == "3" ? "--search-type ${params.mmseqs_searchtype} --strand 2" : "--search-type ${params.mmseqs_searchtype}",
+                "--rescore-mode 3",
+                "--format-output query,target,theader,fident,qlen,tlen,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits" // don't change format-output
+            ]
             publishDir = [
                 path: { "${params.outdir}/consensus/quality_control/mmseqs-search"},
                 mode: params.publish_dir_mode,