From 494648bc592c6190db46f8d32bce34ccbbee467c Mon Sep 17 00:00:00 2001
From: Danilo Di Leo <danilo.dileo@lnu.se>
Date: Tue, 13 Feb 2024 11:38:20 +0100
Subject: [PATCH] removed param eggnog_dbpath from subworkflow

---
 modules/local/eggnog/mapper.nf | 5 ++---
 subworkflows/local/eggnog.nf   | 5 +----
 workflows/metatdenovo.nf       | 2 +-
 3 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/modules/local/eggnog/mapper.nf b/modules/local/eggnog/mapper.nf
index 59701917..8321ff44 100644
--- a/modules/local/eggnog/mapper.nf
+++ b/modules/local/eggnog/mapper.nf
@@ -9,8 +9,7 @@ process EGGNOG_MAPPER {
 
     input:
     tuple val(meta), path(fasta)
-    path(db)
-    path(eggnog_db) // Marker purpose only; to make execution wait for the download process to finish
+    path(eggnog_db), stageAs: 'eggnog/*'
 
     output:
     tuple val(meta), path("*.emapper.hits.gz")                , emit: hits
@@ -37,7 +36,7 @@ process EGGNOG_MAPPER {
     emapper.py \\
         $args \\
         --cpu $task.cpus \\
-        --data_dir $db \\
+        --data_dir eggnog \\
         --output $prefix \\
         -i $input
 
diff --git a/subworkflows/local/eggnog.nf b/subworkflows/local/eggnog.nf
index 2d892848..25efe994 100644
--- a/subworkflows/local/eggnog.nf
+++ b/subworkflows/local/eggnog.nf
@@ -10,17 +10,14 @@ workflow EGGNOG {
     take:
     faa
     collect_fcs
-    dbpath
 
     main:
     ch_versions = Channel.empty()
 
-    ch_dbpath = Channel.fromPath(dbpath, checkIfExists: true)
-
     EGGNOG_DOWNLOAD()
     ch_versions = ch_versions.mix ( EGGNOG_DOWNLOAD.out.versions )
 
-    EGGNOG_MAPPER ( faa, ch_dbpath, EGGNOG_DOWNLOAD.out.eggnog_db )
+    EGGNOG_MAPPER ( faa, EGGNOG_DOWNLOAD.out.all )
     ch_versions = ch_versions.mix ( EGGNOG_MAPPER.out.versions )
 
     EGGNOG_SUM ( EGGNOG_MAPPER.out.emappertsv, collect_fcs )
diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf
index 919a3d0c..e5385254 100644
--- a/workflows/metatdenovo.nf
+++ b/workflows/metatdenovo.nf
@@ -421,7 +421,7 @@ workflow METATDENOVO {
     // SUBWORKFLOW: run eggnog_mapper on the ORF-called amino acid sequences
     //
     if ( ! params.skip_eggnog ) {
-        EGGNOG(ch_protein, ch_fcs_for_summary, params.eggnog_dbpath)
+        EGGNOG(ch_protein, ch_fcs_for_summary)
         ch_versions = ch_versions.mix(EGGNOG.out.versions)
         ch_merge_tables = EGGNOG.out.sumtable
     } else {