From d09808c9c56d31a20f2aac5857d65176032e8d73 Mon Sep 17 00:00:00 2001
From: replikation <christian.jena@gmail.com>
Date: Wed, 10 Jan 2024 12:29:41 +0100
Subject: [PATCH] DB quick fix

---
 workflows/phage_annotation_wf.nf         | 10 +++++-----
 workflows/phage_tax_classification_wf.nf | 21 +++++----------------
 workflows/pprmeta_wf.nf                  |  7 +------
 workflows/sourmash_wf.nf                 | 18 +++---------------
 4 files changed, 14 insertions(+), 42 deletions(-)

diff --git a/workflows/phage_annotation_wf.nf b/workflows/phage_annotation_wf.nf
index 6dff716..fb32e0d 100644
--- a/workflows/phage_annotation_wf.nf
+++ b/workflows/phage_annotation_wf.nf
@@ -17,12 +17,12 @@ workflow phage_annotation_wf {
             //Databases 
             //Database for hmmscan
             // local storage via storeDir
-            if (!params.cloudProcess) { pvog_DB(); db = pvog_DB.out }
+            if (!params.cloudProcess) { pvog_DB(); dbpvog = pvog_DB.out }
             // cloud storage via db_preload.exists()
             if (params.cloudProcess) {
                 db_preload = file("${params.databases}/pvogs/", type: 'dir')
-                if (db_preload.exists()) { db = db_preload }
-                else  { pvog_DB(); db = pvog_DB.out } 
+                if (db_preload.exists()) { dbpvog = db_preload }
+                else  { pvog_DB(); dbpvog = pvog_DB.out } 
             }
             //Vog table
             // local storage via storeDir
@@ -35,9 +35,9 @@ workflow phage_annotation_wf {
             }
             //annotation-process
             prodigal(fasta)
-            if (!params.annotation_db) {hmmscan(prodigal.out, pvog_DB.out)}
+            if (!params.annotation_db) {hmmscan(prodigal.out, dbpvog)}
             else {hmmscan(prodigal.out, annotation_custom_db_ch)}         
-            chromomap_parser(fasta.join(hmmscan.out), vogtable_DB.out)
+            chromomap_parser(fasta.join(hmmscan.out), db)
             chromomap(chromomap_parser.out[0].mix(chromomap_parser.out[1]))
 
             annotationtable_markdown_input = chromomap_parser.out.annotationfile_combined_ch
diff --git a/workflows/phage_tax_classification_wf.nf b/workflows/phage_tax_classification_wf.nf
index e5d8558..64fce02 100644
--- a/workflows/phage_tax_classification_wf.nf
+++ b/workflows/phage_tax_classification_wf.nf
@@ -7,23 +7,12 @@ workflow phage_tax_classification_wf {
     take:   fasta_and_tool_results
     main:    
             fasta = fasta_and_tool_results.map {it -> tuple(it[0],it[1])}
-            // local storage via storeDir
-            if (!params.cloudProcess) { download_references(); db = download_references.out }
-            // cloud storage via db_preload.exists()
-            if (params.cloudProcess) {
-                db_preload = file("${params.databases}/references/phage_references.fa")
-                if (db_preload.exists()) { db = db_preload }
-                else  { download_references(); db = download_references.out }
-            }
+            // get refs
+            download_references()
             // sourmash db build    
-            // local storage via storeDir
-            if (!params.cloudProcess) { sourmash_download_DB(download_references.out); db = sourmash_download_DB.out }
-            // cloud storage via db_preload.exists()
-            if (params.cloudProcess) {
-                db_preload = file("${params.databases}/sourmash/phages.sbt.zip")
-                if (db_preload.exists()) { db = db_preload }
-                else  { sourmash_download_DB(references); db = sourmash_download_DB.out } 
-            }
+            sourmash_download_DB(download_references.out)
+
             sourmash_for_tax(split_multi_fasta_2(fasta), sourmash_download_DB.out).groupTuple(remainder: true)
+            
     emit:   sourmash_for_tax.out
 }
\ No newline at end of file
diff --git a/workflows/pprmeta_wf.nf b/workflows/pprmeta_wf.nf
index 9268a89..d58d065 100644
--- a/workflows/pprmeta_wf.nf
+++ b/workflows/pprmeta_wf.nf
@@ -6,13 +6,8 @@ include { ppr_download_dependencies } from './process/pprmeta/ppr_download_depen
 workflow pprmeta_wf {
     take:   fasta
     main:   if (!params.pp) { 
-                if (!params.cloudProcess) { ppr_download_dependencies(); db = ppr_download_dependencies.out }
+                ppr_download_dependencies()
                 // cloud storage via db_preload.exists()
-                if (params.cloudProcess) {
-                db_preload = file("${params.databases}/pprmeta/PPR-Meta", type: 'dir')
-                if (db_preload.exists()) { db = db_preload }
-                else  { ppr_download_dependencies(); db = ppr_download_dependencies.out } 
-                }
                 
                 filter_PPRmeta(pprmeta(fasta, ppr_download_dependencies.out).groupTuple(remainder: true))
                 // raw data collector
diff --git a/workflows/sourmash_wf.nf b/workflows/sourmash_wf.nf
index 1eaed01..c931784 100644
--- a/workflows/sourmash_wf.nf
+++ b/workflows/sourmash_wf.nf
@@ -10,22 +10,10 @@ workflow sourmash_wf {
     main:   
             if (!params.sm) {
                     // local storage via storeDir
-                    if (!params.cloudProcess) { download_references(); db = download_references.out }
-                    // cloud storage via db_preload.exists()
-                    if (params.cloudProcess) {
-                        db_preload = file("${params.databases}/references/phage_references.fa")
-                        if (db_preload.exists()) { db = db_preload }
-                        else  { download_references(); db = download_references.out }
-                    }
+                    download_references()
                     // sourmash db build    
-                    // local storage via storeDir
-                    if (!params.cloudProcess) { sourmash_download_DB(download_references.out); db = sourmash_download_DB.out }
-                    // cloud storage via db_preload.exists()
-                    if (params.cloudProcess) {
-                        db_preload = file("${params.databases}/sourmash/phages.sbt.zip")
-                        if (db_preload.exists()) { db = db_preload }
-                        else  { sourmash_download_DB(references); db = sourmash_download_DB.out } 
-                    } 
+                    sourmash_download_DB(download_references.out) 
+
                     // sourmash prediction
                     filter_sourmash(sourmash(split_multi_fasta(fasta), sourmash_download_DB.out).groupTuple(remainder: true))
                     // raw data collector