Fix container volume mounts

modules/antismash/antismashlite/main.nf

@@ -7,9 +7,20 @@ process ANTISMASH_ANTISMASHLITE {
         'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
         'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
 
+    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,$modules_dir:/usr/local/lib/python3.8/site-packages/antismash/modules" :
+        workflow.containerEngine == 'docker' ?
+        "-v \$PWD/$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" :
+        ''
+        }
+
     input:
     tuple val(meta), path(sequence_input)
     path(databases)
+    path css_dir
+    path detection_dir
+    path modules_dir
 
     output:
     tuple val(meta), path("${prefix}/clusterblast/*_c*.txt")                 , optional: true, emit: clusterblast_file
@@ -42,13 +53,13 @@ process ANTISMASH_ANTISMASHLITE {
     ## We specifically do not include annotations (--genefinding-tool none) as
     ## this should be run as a separate module for versioning purposes
     antismash \\
-        $sequence_input \\
         $args \\
         -c $task.cpus \\
         --output-dir $prefix \\
         --genefinding-tool none \\
         --logfile $prefix/${prefix}.log \\
-        --databases $databases
+        --databases $databases \\
+        $sequence_input
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/antismash/antismashlite/meta.yml

@@ -37,6 +37,21 @@ input:
       type: directory
       description: downloaded antismash databases e.g. data/databases
       pattern: "*"
+  - css_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"
 
 output:
   - meta:

tests/modules/antismash/antismashlite/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-//include { GUNZIP } from '../../../modules/gunzip/main.nf'
+include { GUNZIP } from '../../../modules/gunzip/main.nf'
 include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
 include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
 include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
@@ -10,40 +10,57 @@ include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/anti
 include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
 include { PROKKA } from '../../../modules/prokka/main.nf'
 
-workflow test_antismashlite {
+// workflow test_antismashlite {
-    input = [
+//     input = [
-        [ id:'test' ], // meta map
+//         [ id:'test' ], // meta map
-        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
+//         file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
+
+//     input_antismash_db1 = [
+//         [],
+//         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+//     ]
+
+//     input_antismash_db2 = [
+//         [],
+//         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+//     ]
+
+//     input_antismash_db3 = [
+//         [],
+//         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+//     ]
+
+//     UNTAR1 ( input_antismash_db1 )
+//     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] } )
+//}
+
+workflow test_prokka_antismashlite {
+    input_gunzip = [ [ id:'test' ], // meta map
+            file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]
 
     input_antismash_db1 = [
         [],
         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
     ]
 
-        input_antismash_db2 = [
+    input_antismash_db2 = [
         [],
         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
     ]
 
-        input_antismash_db3 = [
+    input_antismash_db3 = [
         [],
         file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
     ]
 
+    GUNZIP ( input_gunzip )
+    PROKKA ( GUNZIP.out.gunzip, [], [] )
     UNTAR1 ( input_antismash_db1 )
     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 )
+    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] } )
 }
-
-//workflow test_prokka_antismashlite {
-//     input_gunzip = [ [ id:'test' ], // meta map
-//             file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]
-
-//     GUNZIP ( input_gunzip )
-//     PROKKA ( GUNZIP.out.gunzip, [], [] )
-//     ANTISMASHLITEDOWNLOADDATABASES ()
-//     ANTISMASH ( PROKKA.out.gbk )
-// }
-

tests/modules/antismash/antismashlite/test.yml

@@ -1,5 +1,5 @@
 - name: antismash antismashlite test_antismashlite
-  command: nextflow run ./tests/modules/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config
+  command: nextflow run tests/modules/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config
   tags:
     - antismash/antismashlite
     - antismash
@@ -16,7 +16,7 @@
       contains: ['{"version": "6.0.1", "input_file": "genome.gbff.gz", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
     - path: output/antismash/test/genome.zip
     - path: output/antismash/test/index.html
-      md5sum: 4792f0f4faf318035fbec5b4bf0ff76e
+      md5sum: 32aaf51315258af3b300d9a5bafd7bdc
     - path: output/antismash/test/js/antismash.js
       md5sum: 58e90c3d783ae014cc3d51849bcb50a2
     - path: output/antismash/test/js/jquery.js
@@ -30,8 +30,76 @@
     - path: output/antismash/versions.yml
       md5sum: 7151dfd4d39173338397b2dab50acf8e
     - path: output/untar1/versions.yml
-      md5sum: 42c2c02eb6b5bc47b151bdd2c49bbb2d
+      md5sum: 1e4721017721c45370996318e6b807e5
     - path: output/untar2/versions.yml
-      md5sum: 5a608b991b7d3e55cc43206939991a2d
+      md5sum: a6ae4977a432f3c5ef26687cec8622de
     - path: output/untar3/versions.yml
-      md5sum: ec74401950e3820b7575840571a6f00c
+      md5sum: a5ee00c1c426ed601ff654891ba0f645
+
+- 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
+  files:
+    - path: output/antismash/test/NZ_CP069563.1.region001.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/NZ_CP069563.1.region002.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/css/bacteria.css
+      md5sum: 8b3c2f8b143d5245a5f42f55803c532c
+    - path: output/antismash/test/index.html
+      md5sum: 3773c3ec61fb1e8cd9a67791b37d9b79
+    - path: output/antismash/test/js/antismash.js
+      md5sum: 58e90c3d783ae014cc3d51849bcb50a2
+    - path: output/antismash/test/js/jquery.js
+      md5sum: 397754ba49e9e0cf4e7c190da78dda05
+    - path: output/antismash/test/js/jquery.tablesorter.min.js
+      md5sum: 5e9e08cef4d1be0eaa538e6eb28809a7
+    - path: output/antismash/test/regions.js
+      contains: [ '"seq_id": "NZ_CP069563.1"' ]
+    - path: output/antismash/test/test.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/test.json
+      contains: ['"id": "NZ_CP069563.1"']
+    - path: output/antismash/test/test.log
+      contains: ['antiSMASH status: SUCCESS']
+    - path: output/antismash/test/test.zip
+    - path: output/antismash/versions.yml
+      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
+      md5sum: 8fefbfa7860f280cc881c3a3b377d6da
+    - path: output/prokka/test/test.ffn
+      md5sum: 9c4d4d7dc28625bcb13c6fbd27ca13c3
+    - path: output/prokka/test/test.fna
+      md5sum: 96aa7707b864499745e8946f169ae8e0
+    - path: output/prokka/test/test.fsa
+      md5sum: dbe7d3d43d46920802d2aec5cd177ddc
+    - path: output/prokka/test/test.gbk
+      md5sum: 286ea011a64c0d281de3981ed2f296ff
+    - path: output/prokka/test/test.gff
+      md5sum: 9f733b702454e7750b7d4686369fe7e4
+    - path: output/prokka/test/test.log
+      contains: ["Annotation finished successfully."]
+    - path: output/prokka/test/test.sqn
+      md5sum: a901ac190675f976e373219f0191d067
+    - path: output/prokka/test/test.tbl
+      md5sum: 98f3b705f47b40255631ae43823e8271
+    - path: output/prokka/test/test.tsv
+      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