From 407d0bb752da0b97f8596e39fe29c012dbd08fd5 Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Sun, 17 Apr 2022 11:22:23 -0400
Subject: [PATCH] update motus_downloaddb

---
 modules/motus/downloaddb/main.nf  | 11 ++++++-----
 modules/motus/downloaddb/meta.yml |  6 ++++--
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/modules/motus/downloaddb/main.nf b/modules/motus/downloaddb/main.nf
index 0456b471..928b1294 100644
--- a/modules/motus/downloaddb/main.nf
+++ b/modules/motus/downloaddb/main.nf
@@ -11,23 +11,24 @@ process MOTUS_DOWNLOADDB {
 
     output:
     path "db_mOTU/"                , emit: db
-    path "versions.yml"           , emit: versions
+    path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args     = task.ext.args ?: ''
+    def software = ${motus_downloaddb.simpleName}_copy.py
     """
     ## must copy file to working directory,
     ## otherwise the reference_db will be download to bin folder
     ## other than current directory
-    cp $motus_downloaddb ${motus_downloaddb.simpleName}_copy.py
-    python ${motus_downloaddb.simpleName}_copy.py \\
+    cp $motus_downloaddb ${software}
+    python ${software} \\
         $args \\
         -t $task.cpus
     ## clean up
-    rm ${motus_downloaddb.simpleName}_copy.py
+    rm ${software}
 
     ## mOTUs version number is not available from command line.
     ## mOTUs save the version number in index database folder.
diff --git a/modules/motus/downloaddb/meta.yml b/modules/motus/downloaddb/meta.yml
index 1fa5e220..2d363cb1 100644
--- a/modules/motus/downloaddb/meta.yml
+++ b/modules/motus/downloaddb/meta.yml
@@ -5,6 +5,8 @@ keywords:
   - metagenomics
   - fastq
   - taxonomic profiling
+  - database
+  - download
 tools:
   - "motus":
       description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
@@ -19,7 +21,7 @@ input:
       type: file
       description: |
         the mOTUs downloadDB script source file
-      pattern: "*{.py}"
+      pattern: "downloadDB.py"
 
 output:
   - versions:
@@ -27,7 +29,7 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - db:
-      type: file
+      type: directory
       description: The mOTUs database
       pattern: "db_mOTU"