Antismash db output patch 1 (#3)

* Update main.nf

* Update meta.yml

* Update test.yml

modules/antismash/antismashlitedownloaddatabases/main.nf

@@ -27,9 +27,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     output:
     path("antismash_db") , emit: database
-    path("css"), emit: css_dir
+    path("antismash_dir"), emit: antismash_dir
-    path("detection"), emit: detection_dir
-    path("modules"), emit: modules_dir
     path "versions.yml", emit: versions
 
     when:
@@ -42,6 +40,8 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
         --database-dir antismash_db \\
         $args
 
+    cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         antismash-lite: \$(antismash --version | sed 's/antiSMASH //')

modules/antismash/antismashlitedownloaddatabases/meta.yml

@@ -27,7 +27,7 @@ input:
   - database_css:
       type: directory
       description: |
-        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by ther use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
       pattern: "css"
   - database_detection:
       type: directory
@@ -50,21 +50,11 @@ output:
       type: directory
       description: Download directory for antiSMASH databases
       pattern: "antismash_db"
-  - css_dir:
+  - antismash_dir:
       type: directory
       description: |
-        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.
-      pattern: "css"
+      pattern: "antismash_dir"
-  - detection_dir:
-      type: directory
-      description: |
-        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "detection"
-  - modules_dir:
-      type: directory
-      description: |
-        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "modules"
 
 authors:
   - "@jasmezz"

tests/modules/antismash/antismashlitedownloaddatabases/test.yml

@@ -1,17 +1,16 @@
 - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
   command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
   tags:
-    - antismash
     - antismash/antismashlitedownloaddatabases
+    - antismash
   files:
     - path: output/antismash/versions.yml
-      md5sum: 24859c67023abab99de295d3675a24b6
+      md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3
     - path: output/antismash/antismash_db
     - path: output/antismash/antismash_db/clusterblast
     - path: output/antismash/antismash_db/clustercompare
     - path: output/antismash/antismash_db/pfam
     - path: output/antismash/antismash_db/resfam
     - path: output/antismash/antismash_db/tigrfam
-    - path: output/antismash/css
+    - path: output/antismash/antismash_dir
-    - path: output/antismash/detection
+    - path: output/antismash/antismash_dir/detection/hmm_detection/data/bgc_seeds.hmm
-    - path: output/antismash/modules