Merge pull request #35 from avantonder/dev

Update multiqc file names
nf-core · May 7, 2021 · df7fa7c · df7fa7c
2 parents 8f719c0 + 1af026f
commit df7fa7c
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -87,7 +87,7 @@ params {
             args = '--all --model GTR+G --bs-trees 1000'
             publish_dir = 'raxmlng'
         }
-        'bactmap_multiqc' {
+        'multiqc' {
             args = ''
             publish_files   = ['_data':'', 'html':'']
             publish_dir     = 'multiqc'

diff --git a/modules/local/multiqc_bactmap.nf → modules/local/multiqc.nf b/modules/local/multiqc_bactmap.nf → modules/local/multiqc.nf
diff --git a/workflows/bactmap.nf b/workflows/bactmap.nf
@@ -29,14 +29,14 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
 // Don't overwrite global params.modules, create a copy instead and use that within the main script.
 def modules = params.modules.clone()
 
-def multiqc_options   = modules['bactmap_multiqc']
+def multiqc_options   = modules['multiqc']
 multiqc_options.args += params.multiqc_title ? Utils.joinModuleArgs(["--title \"$params.multiqc_title\""]) : ''
 
 // Local: Modules
 include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions'     addParams( options: [publish_files : ['csv':'']] )
 include { VCF2PSEUDOGENOME      } from '../modules/local/vcf2pseudogenome'          addParams( options: modules['vcf2pseudogenome'])
 include { ALIGNPSEUDOGENOMES } from '../modules/local/alignpseudogenomes'           addParams( options: modules['alignpseudogenomes'])
-include { MULTIQC               } from '../modules/local/multiqc_bactmap'           addParams( options: multiqc_options )
+include { MULTIQC               } from '../modules/local/multiqc'                   addParams( options: multiqc_options )
 
 // nf-core: Modules
 include { GUBBINS } from '../modules/nf-core/software/gubbins/main'                 addParams( options: modules['gubbins'])