Update ANTISMASH to 6.1.1 and enable_conda replacement

modules/nf-core/antismash/antismashlite/main.nf

@@ -2,10 +2,10 @@ process ANTISMASH_ANTISMASHLITE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::antismash-lite=6.0.1"
+    conda "bioconda::antismash-lite=6.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
-        'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/antismash-lite:6.1.1--pyhdfd78af_0' :
+        'quay.io/biocontainers/antismash-lite:6.1.1--pyhdfd78af_0' }"
 
     containerOptions {
         workflow.containerEngine == 'singularity' ?

modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf

@@ -1,10 +1,10 @@
 process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
     label 'process_single'
 
-    conda "bioconda::antismash-lite=6.0.1"
+    conda "bioconda::antismash-lite=6.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
-        'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/antismash-lite:6.1.1--pyhdfd78af_0' :
+        'quay.io/biocontainers/antismash-lite:6.1.1--pyhdfd78af_0' }"
 
     /*
     These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input 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. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
@@ -35,18 +35,30 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     script:
     def args = task.ext.args ?: ''
-    conda = params.enable_conda
+    cp_cmd = session.config.conda.enabled ? "cp -r \$(python -c 'import antismash;print(antismash.__file__.split(\"/__\")[0])') antismash_dir;" : "cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir;"
     """
     download-antismash-databases \\
         --database-dir antismash_db \\
         $args
 
-    if [[ $conda = false ]]; \
-        then \
-            cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir; \
-        else \
-            cp -r \$(python -c 'import antismash;print(antismash.__file__.split("/__")[0])') antismash_dir; \
-    fi
+    $cp_cmd
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    cp_cmd = session.config.conda.enabled ? "cp -r \$(python -c 'import antismash;print(antismash.__file__.split(\"/__\")[0])') antismash_dir;" : "cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir;"
+    """
+    echo "download-antismash-databases --database-dir antismash_db $args"
+
+    echo "$cp_cmd"
+
+    mkdir antismash_dir
+    mkdir antismash_db
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml

@@ -1,5 +1,5 @@
 name: antismash_antismashlitedownloaddatabases
-description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases.
+description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.
 keywords:
   - secondary metabolites
   - BGC

tests/modules/nf-core/antismash/antismashlite/main.nf

@@ -21,19 +21,20 @@ workflow test_antismashlite {
         file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
     ]
 
+    // hash 91bb8781c576967e23d2c5315dd4d43213575033 is for antismash version 6.1.1
     antismash_css = [
         [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+        file('https://github.com/nf-core/test-datasets/raw/91bb8781c576967e23d2c5315dd4d43213575033/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
     ]
 
     antismash_detection = [
         [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+        file('https://github.com/nf-core/test-datasets/raw/91bb8781c576967e23d2c5315dd4d43213575033/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
     ]
 
     antismash_modules = [
         [],
-        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+        file('https://github.com/nf-core/test-datasets/raw/91bb8781c576967e23d2c5315dd4d43213575033/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
     ]
 
     GUNZIP1 ( genome_fna )

tests/modules/nf-core/antismash/antismashlite/test.yml

@@ -1,35 +1,97 @@
 - name: antismash antismashlite test_antismashlite
-  command: nextflow run ./tests/modules/nf-core/antismash/antismashlite -entry test_antismashlite -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/antismash/antismashlite -entry test_antismashlite -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/antismash/antismashlite/nextflow.config
   tags:
-    - antismash/antismashlite
     - antismash
+    - antismash/antismashlite
   files:
     - path: output/antismash/test/NZ_CP069563.1.region001.gbk
-      contains: ['/tool="antismash"']
+      contains:
+        - "##antiSMASH-Data-END##"
     - path: output/antismash/test/NZ_CP069563.1.region002.gbk
-      contains: ['/tool="antismash"']
+      contains:
+        - "##antiSMASH-Data-END##"
     - path: output/antismash/test/css/bacteria.css
-      md5sum: 8b3c2f8b143d5245a5f42f55803c532c
+      md5sum: d9c34889e2a676442ad5301d88b1b425
     - path: output/antismash/test/genome.gbk
-      contains: ['/tool="antismash"']
+      contains:
+        - "##antiSMASH-Data-END##"
     - path: output/antismash/test/genome.json
-      contains: ['{"version": "6.0.1", "input_file": "genome.fna", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
+      contains:
+        - "genome.fna"
+        - "records"
     - path: output/antismash/test/genome.zip
+    - path: output/antismash/test/images/about.svg
+      md5sum: 2573f954dd506e2d0878daed04f5420a
+    - path: output/antismash/test/images/bacteria_about.png
+      md5sum: 99cdc2aa09aee37553b10ca86b172170
+    - path: output/antismash/test/images/bacteria_antismash_icon.svg
+      md5sum: 23a265b0e1cf293a4743fe13030b636f
+    - path: output/antismash/test/images/bacteria_antismash_logo.svg
+      md5sum: f80f639969ee6506571ffda2e197df93
+    - path: output/antismash/test/images/bacteria_antismash_white.svg
+      md5sum: 2c9da15cc168d8f796269d037b5e7f60
+    - path: output/antismash/test/images/bacteria_download.png
+      md5sum: c3428df1cf17cb97e2897ca6daa93d48
+    - path: output/antismash/test/images/bacteria_help.png
+      md5sum: 359b68f90c73208eb389759c0f5c1091
+    - path: output/antismash/test/images/bacteria_home.png
+      md5sum: 6595d97ee49d251fe038207f82012eff
+    - path: output/antismash/test/images/bacteria_logo.png
+      md5sum: 013f84d6dd93cde96f07084ff63d855c
+    - path: output/antismash/test/images/contact.svg
+      md5sum: 53b878c2af4f8a80a647ac30f61e6bf6
+    - path: output/antismash/test/images/download.svg
+      md5sum: 722038156f4ece46747cbf6908501974
+    - path: output/antismash/test/images/expand-arrows-alt-solid.svg
+      md5sum: 21b37749f54320135a455ed266a7fc3a
+    - path: output/antismash/test/images/external-link-alt-solid.svg
+      md5sum: ca337694c74e57f73d15ca9db30081ba
+    - path: output/antismash/test/images/fungi_about.png
+      md5sum: 4d55bf14df0340dca01a286487fa8448
+    - path: output/antismash/test/images/fungi_antismash_icon.svg
+      md5sum: 2acc19cc91d5d7285a72f0b3912e108a
+    - path: output/antismash/test/images/fungi_antismash_icon_white.svg
+      md5sum: 961f1c41e25036a625f115f209a961c7
+    - path: output/antismash/test/images/fungi_antismash_logo.svg
+      md5sum: 36560983a36f46786c98a05125b15724
+    - path: output/antismash/test/images/fungi_download.png
+      md5sum: 782580852674aab0b69b2b94a94c7615
+    - path: output/antismash/test/images/fungi_help.png
+      md5sum: 0ac06748f3177d150ab90997117c4f64
+    - path: output/antismash/test/images/fungi_home.png
+      md5sum: 880071898062d6dafe989ac73bb7bbea
+    - path: output/antismash/test/images/fungi_logo.png
+      md5sum: 29294392a3953fd1ba12d1a39cebaeeb
+    - path: output/antismash/test/images/help.svg
+      md5sum: e7565a3cd74893422f2886a0af748df2
+    - path: output/antismash/test/images/mail.png
+      md5sum: 049f51233b29663e4e4e4c8097c2d096
+    - path: output/antismash/test/images/minus-circle.svg
+      md5sum: b523305570d06b6e34cd7099bed22015
+    - path: output/antismash/test/images/nostructure_icon.png
+      md5sum: fc982a5b84a1a99db607731625a87f88
+    - path: output/antismash/test/images/plant_antismash_icon.svg
+      md5sum: e031de9570ef2809e52502481a5e77ea
+    - path: output/antismash/test/images/plant_antismash_icon_white.svg
+      md5sum: 10d25996b023dbdaed4a382471ab4877
+    - path: output/antismash/test/images/plus-circle.svg
+      md5sum: cba2cdd9ef893274f572228b354718cf
+    - path: output/antismash/test/images/question-circle-solid.svg
+      md5sum: 6dbc83547e29ecedc7f2a5b81354353b
+    - path: output/antismash/test/images/search-solid.svg
+      md5sum: aeab848c26357f3d120f3e58f1efa8f5
     - path: output/antismash/test/index.html
-      md5sum: de787e865c3a1eec143a19d2facb4de4
+      md5sum: 471f04db1e7c6e055bc0892fe1f637a4
     - path: output/antismash/test/js/antismash.js
-      md5sum: 58e90c3d783ae014cc3d51849bcb50a2
+      md5sum: 55a3f55e1eb5d6ab3fa73d867da12bbd
     - 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"']
+      contains:
+        - '"seq_id": "NZ_CP069563.1"'
     - path: output/antismash/test/test.log
-      contains: ["antiSMASH version: 6.0.1"]
+      contains:
+        - "antiSMASH status: SUCCESS"
     - path: output/antismash/versions.yml
-      md5sum: 759431a43da33e2ef8e2d0ebd79a439b
-    - path: output/gunzip1/genome.fna
-      md5sum: dafd38f5454b54fbea38245d773062a5
-    - path: output/gunzip2/genome.gff
-      md5sum: 9b9c848b1946d43fa68128f4d6316052

tests/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf

@@ -8,23 +8,27 @@ include { UNTAR as UNTAR3 } from '../../../../../modules/nf-core/untar/main.nf'
 include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../../../modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf'
 
 workflow test_antismash_antismashlitedownloaddatabases {
-    // hash 9d816b1327c5f73cd0113af0966197db1956c840 is additional files for for antismash-lite 6.0.1
-    input1 = [
+
+    // hash 91bb8781c576967e23d2c5315dd4d43213575033 is for antismash version 6.1.1
+    antismash_css = [
         [],
-        file('https://github.com/nf-core/test-datasets/raw/9d816b1327c5f73cd0113af0966197db1956c840/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+        file('https://github.com/nf-core/test-datasets/raw/91bb8781c576967e23d2c5315dd4d43213575033/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
     ]
-    input2 = [
+
+    antismash_detection = [
         [],
-        file('https://github.com/nf-core/test-datasets/raw/9d816b1327c5f73cd0113af0966197db1956c840/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+        file('https://github.com/nf-core/test-datasets/raw/91bb8781c576967e23d2c5315dd4d43213575033/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
     ]
-    input3 = [
+
+    antismash_modules = [
         [],
-        file('https://github.com/nf-core/test-datasets/raw/9d816b1327c5f73cd0113af0966197db1956c840/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+        file('https://github.com/nf-core/test-datasets/raw/91bb8781c576967e23d2c5315dd4d43213575033/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
     ]
 
-    UNTAR1 ( input1 )
-    UNTAR2 ( input2 )
-    UNTAR3 ( input3 )
+
+    UNTAR1 ( antismash_css )
+    UNTAR2 ( antismash_detection )
+    UNTAR3 ( antismash_modules )
 
     ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
 }

tests/modules/nf-core/antismash/antismashlitedownloaddatabases/test.yml

@@ -4,8 +4,6 @@
     - antismash/antismashlitedownloaddatabases
     - antismash
   files:
-    - path: output/antismash/versions.yml
-      md5sum: 24859c67023abab99de295d3675a24b6
     - path: output/antismash/antismash_db
     - path: output/antismash/antismash_db/clusterblast
     - path: output/antismash/antismash_db/clustercompare