Simplify/reduce container mount volumes

modules/antismash/antismashlite/main.nf

@@ -9,18 +9,16 @@ process ANTISMASH_ANTISMASHLITE {
 
     containerOptions {
         workflow.containerEngine == 'singularity' ?
-        "-B $css_dir:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css,$detection_dir:/usr/local/lib/python3.8/site-packages/antismash/detection,$modules_dir:/usr/local/lib/python3.8/site-packages/antismash/modules" :
+        "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
         workflow.containerEngine == 'docker' ?
-        "-v \$PWD/$css_dir:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css -v \$PWD/$detection_dir:/usr/local/lib/python3.8/site-packages/antismash/detection -v \$PWD/$modules_dir:/usr/local/lib/python3.8/site-packages/antismash/modules" :
+        "-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
         ''
         }
 
     input:
     tuple val(meta), path(sequence_input)
     path(databases)
-    path css_dir
-    path detection_dir
-    path modules_dir
+    path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
 
     output:
     tuple val(meta), path("${prefix}/clusterblast/*_c*.txt")                 , optional: true, emit: clusterblast_file

modules/antismash/antismashlite/meta.yml

@@ -37,21 +37,11 @@ input:
       type: directory
       description: downloaded antismash databases e.g. data/databases
       pattern: "*"
-  - 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 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"
-  - 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 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: "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 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: "modules"
+        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 within antismash-lite. As this folder cannot be modified within the docker and singularity containers, it needs to be mounted (including all modified files from the downloading step) as a workaround.
+      pattern: "*"
 
 output:
   - meta:

tests/modules/antismash/antismashlite/main.nf

@@ -11,7 +11,7 @@ include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismas
 include { PROKKA } from '../../../modules/prokka/main.nf'
 
 workflow test_antismashlite {
-    input = [
+    input_genome = [
         [ id:'test' ], // meta map
         file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
 
@@ -34,7 +34,7 @@ workflow test_antismashlite {
     UNTAR2 ( input_antismash_db2 )
     UNTAR3 ( input_antismash_db3 )
     ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
-    ANTISMASH_ANTISMASHLITE ( input, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
+    ANTISMASH_ANTISMASHLITE ( input_genome, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, [] )
 }
 
 workflow test_prokka_antismashlite {
@@ -62,5 +62,5 @@ workflow test_prokka_antismashlite {
     UNTAR2 ( input_antismash_db2 )
     UNTAR3 ( input_antismash_db3 )
     ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
-    ANTISMASH_ANTISMASHLITE ( PROKKA.out.gbk, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
+    ANTISMASH_ANTISMASHLITE ( PROKKA.out.gbk, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir )
 }

tests/modules/antismash/antismashlite/test.yml

@@ -24,23 +24,17 @@
     - path: output/antismash/test/js/jquery.tablesorter.min.js
       md5sum: 5e9e08cef4d1be0eaa538e6eb28809a7
     - path: output/antismash/test/regions.js
-      md5sum: dfc82025379d87df63fbfce734e67725
+      contains: ['"seq_id": "NZ_CP069563.1"']
     - path: output/antismash/test/test.log
       contains: ['antiSMASH version: 6.0.1']
     - path: output/antismash/versions.yml
-      md5sum: 7151dfd4d39173338397b2dab50acf8e
-    - path: output/untar1/versions.yml
-      md5sum: 1e4721017721c45370996318e6b807e5
-    - path: output/untar2/versions.yml
-      md5sum: a6ae4977a432f3c5ef26687cec8622de
-    - path: output/untar3/versions.yml
-      md5sum: a5ee00c1c426ed601ff654891ba0f645
+      md5sum: 759431a43da33e2ef8e2d0ebd79a439b
 
 - name: antismash antismashlite test_prokka_antismashlite
   command: nextflow run tests/modules/antismash/antismashlite -entry test_prokka_antismashlite -c tests/config/nextflow.config
   tags:
-    - antismash
     - antismash/antismashlite
+    - antismash
   files:
     - path: output/antismash/test/NZ_CP069563.1.region001.gbk
       contains: ['/tool="antismash"']
@@ -69,8 +63,6 @@
       md5sum: da6bed0032d0f7ad4741e0074ad6b1ff
     - path: output/gunzip/genome.fna
       md5sum: dafd38f5454b54fbea38245d773062a5
-    - path: output/gunzip/versions.yml
-      md5sum: 93ce587e93791c8cf500482d42b6069f
     - path: output/prokka/test/test.err
       md5sum: 194fd8a1d1cde9919841a1afd4414760
     - path: output/prokka/test/test.faa
@@ -95,11 +87,3 @@
       md5sum: 26e8aa4b2212f320e82b6db7c93d4461
     - path: output/prokka/test/test.txt
       md5sum: aea5834a64dff02d3588cecbe25c3914
-    - path: output/prokka/versions.yml
-      md5sum: 286ac10895a9f26ee8dd933dbc5d2b1c
-    - path: output/untar1/versions.yml
-      md5sum: 6c1bfedb010be6dfee273aa267b1cae3
-    - path: output/untar2/versions.yml
-      md5sum: 65db3fe9c809e5371158deae444fb343
-    - path: output/untar3/versions.yml
-      md5sum: 713d3aa0ee24ff680a8024cc53765d60