refactor: Remove phispy info from report (#128)

* refactor: Remove phispy info from report * fix: Add concatenated core_genome to output * fix: Remove duplicated import
beiko-lab · Jun 13, 2023 · 82bb3f8 · 82bb3f8
1 parent d78dfc9
commit 82bb3f8
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -367,6 +367,14 @@ process {
         ]
     }
 
+    withName: CONCAT_ALIGNMENT {
+        publishDir = [
+            path: { "${params.outdir}/pangenomics/ppanggolin" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('core_gene_alignment.aln') ? filename : null }
+        ]
+    }
+
     // phylogenomics
     withName: IQTREE {
         publishDir = [

diff --git a/subworkflows/local/annotation.nf b/subworkflows/local/annotation.nf
@@ -29,7 +29,6 @@ include { RGI;
 include { MOB_RECON } from '../../modules/local/mobsuite'
 include { ISLANDPATH } from '../../modules/local/islandpath/main'
 include { PHISPY } from '../../modules/nf-core/phispy/main'
-include { PHISPY } from '../../modules/nf-core/phispy/main'
 include { INTEGRON_FINDER } from '../../modules/local/integronfinder/main.nf'
 include { CONCAT_OUTPUT as CONCAT_PROKKA;
           CONCAT_OUTPUT as CONCAT_BAKTA;
@@ -239,7 +238,6 @@ workflow ANNOTATE_ASSEMBLIES {
                 .set { phispy_tsvs }
 
             CONCAT_PHISPY(phispy_tsvs, "PHISPY", 1)
-            CONCAT_PHISPY.out.txt.set{ ch_phispy_out }
         }
 
         ISLANDPATH(ch_gbk_files)