From 0b3da14468c2669947e9f185a0b953e0d2099c20 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <matricaria.suaveolens@gmail.com>
Date: Fri, 9 Feb 2024 10:43:05 +0100
Subject: [PATCH] Finalize eggnog download/map rework

---
 modules/local/eggnog/download.nf | 13 ++++++++-----
 modules/local/eggnog/mapper.nf   |  1 +
 nextflow.config                  |  1 -
 nextflow_schema.json             |  9 +--------
 subworkflows/local/eggnog.nf     | 20 ++++++--------------
 workflows/metatdenovo.nf         |  5 +----
 6 files changed, 17 insertions(+), 32 deletions(-)

diff --git a/modules/local/eggnog/download.nf b/modules/local/eggnog/download.nf
index b070f538..ffca10e4 100644
--- a/modules/local/eggnog/download.nf
+++ b/modules/local/eggnog/download.nf
@@ -8,22 +8,25 @@ process EGGNOG_DOWNLOAD {
         'biocontainers/eggnog-mapper:2.1.9--pyhdfd78af_0' }"
 
     input:
-    //path "eggnog_dbpath"
 
     output:
-    path("eggnog_db")  , emit: db
-    path "versions.yml", emit: versions
+    path "eggnog.db"                  , emit: eggnog_db
+    path "eggnog_proteins.dmnd"       , emit: dmnd
+    path "eggnog.taxa.db"             , emit: taxa_db
+    path "eggnog.taxa.db.traverse.pkl", emit: pkl
+    path "*"                          , emit: all
+    path "versions.yml"               , emit: versions, optional: true // Optional to allow skipping if this is the only file that's missing
 
     script:
     def args = task.ext.args ?: ''
 
     """
-    mkdir eggnog_db
+    #mkdir eggnog_db
 
     download_eggnog_data.py \\
         $args \\
         -y \\
-        --data_dir eggnog_db
+        --data_dir .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/eggnog/mapper.nf b/modules/local/eggnog/mapper.nf
index 6e0dd2fe..59701917 100644
--- a/modules/local/eggnog/mapper.nf
+++ b/modules/local/eggnog/mapper.nf
@@ -10,6 +10,7 @@ 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
 
     output:
     tuple val(meta), path("*.emapper.hits.gz")                , emit: hits
diff --git a/nextflow.config b/nextflow.config
index 2770b02f..365f764e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -59,7 +59,6 @@ params {
 
     // Eggnog options
     eggnog_dbpath               = 'eggnog'
-    create_eggnogdb             = false
     skip_eggnog                 = false
 
     // KOfamscan options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index d3e30390..ed156e20 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -264,14 +264,7 @@
                     "default": "eggnog",
                     "description": "Specify EGGNOG database path",
                     "fa_icon": "far fa-file-code",
-                    "help_text": "This parameter specifies where you have an EGGNOG database, or, where it will be created using the --create_eggnog_db parameter."
-                },
-                "create_eggnogdb": {
-                    "type": "boolean",
-                    "default": false,
-                    "fa_icon": "fas fa-forward",
-                    "description": "create an EGGNOG database",
-                    "help_text": "Use this parameter if you want to download the EGGNOG database."
+                    "help_text": "This parameter specifies where you have an EGGNOG database, or, where it will be created using the --create_eggnog_db parameter. The directory must exist."
                 },
                 "skip_kofamscan": {
                     "type": "boolean",
diff --git a/subworkflows/local/eggnog.nf b/subworkflows/local/eggnog.nf
index 553fe333..2d892848 100644
--- a/subworkflows/local/eggnog.nf
+++ b/subworkflows/local/eggnog.nf
@@ -11,24 +11,16 @@ workflow EGGNOG {
     faa
     collect_fcs
     dbpath
-    createdb
 
     main:
     ch_versions = Channel.empty()
 
-    if ( createdb ) {
-        // Not allowed, or?
-        if ( ! file(dbpath).exists() ) {
-            file(dbpath).mkdir()
-        }
-        EGGNOG_DOWNLOAD( )
-        ch_dbpath = EGGNOG_DOWNLOAD.out.db
-        ch_versions = ch_versions.mix ( EGGNOG_DOWNLOAD.out.versions )
-    } else {
-        ch_dbpath = Channel.fromPath(dbpath, checkIfExists: true)
-    }
-
-    EGGNOG_MAPPER ( faa, ch_dbpath )
+    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 )
     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 0a7dccf7..1d5d9fbe 100644
--- a/workflows/metatdenovo.nf
+++ b/workflows/metatdenovo.nf
@@ -420,11 +420,8 @@ workflow METATDENOVO {
     //
     // SUBWORKFLOW: run eggnog_mapper on the ORF-called amino acid sequences
     //
-    //ch_eggnog_dbpath   = Channel.fromPath(params.eggnog_dbpath, checkIfExists: true)
-    //ch_create_eggnogdb = Channel.of(params.create_eggnogdb)
     if ( ! params.skip_eggnog ) {
-        //EGGNOG(ch_protein, ch_fcs_for_summary, ch_eggnog_dbpath, ch_create_eggnogdb )
-        EGGNOG(ch_protein, ch_fcs_for_summary, params.eggnog_dbpath, params.create_eggnogdb )
+        EGGNOG(ch_protein, ch_fcs_for_summary, params.eggnog_dbpath)
         ch_versions = ch_versions.mix(EGGNOG.out.versions)
         ch_merge_tables = EGGNOG.out.sumtable
     } else {