Remove prokka test workflow

modules/antismash/antismashlite/main.nf

@@ -64,31 +64,4 @@ process ANTISMASH_ANTISMASHLITE {
         antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
     END_VERSIONS
     """
-
-    stub:
-    """
-    mkdir ${prefix}
-    touch ${prefix}/clusterblast/stub_c.stub.txt
-    touch ${prefix}/css/stub.css
-    touch ${prefix}/images
-    touch ${prefix}/js/stub.js
-    touch ${prefix}/knownclusterblast/regionstub/ctg.stub.html
-    touch ${prefix}/knownclusterblast/stub._c.stub.txt
-    touch ${prefix}/svg/clusterblast.stub.svg
-    touch ${prefix}/svg/knownclusterblast.stub.svg
-    touch ${prefix}/stub.gbk
-    touch ${prefix}/stub.json
-    touch ${prefix}/stub.log
-    touch ${prefix}/stub.zip
-    touch ${prefix}/stub.region.stub.gbk
-    touch ${prefix}/clusterblastoutput.txt
-    touch ${prefix}/index.html
-    touch ${prefix}/knownclusterblastoutput.txt
-    touch ${prefix}/regions.js
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
-    END_VERSIONS
-    """
 }

tests/modules/antismash/antismashlite/main.nf

@@ -2,30 +2,11 @@
 
 nextflow.enable.dsl = 2
 
-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'
 include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
 include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
-include { PROKKA } from '../../../modules/prokka/main.nf'
-
-process STUB_ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
-    input:
-    path database_css
-    path database_detection
-    path database_modules
-
-    output:
-    path("antismash_db") , emit: database
-    path("antismash_dir"), emit: antismash_dir
-
-    stub:
-    """
-    mkdir antismash_db
-    mkdir antismash_dir
-    """
-}
 
 workflow test_antismashlite {
     input_genome = [
@@ -53,31 +34,3 @@ workflow test_antismashlite {
     ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( 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, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir )
 }
-
-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 = [
-        [],
-        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)
-    ]
-
-    GUNZIP ( input_gunzip )
-    PROKKA ( GUNZIP.out.gunzip, [], [] )
-    UNTAR1 ( input_antismash_db1 )
-    UNTAR2 ( input_antismash_db2 )
-    UNTAR3 ( input_antismash_db3 )
-    STUB_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, STUB_ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, STUB_ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir )
-}

tests/modules/antismash/antismashlite/test.yml

@@ -13,7 +13,8 @@
     - path: output/antismash/test/genome.gbk
       contains: ['/tool="antismash"']
     - path: output/antismash/test/genome.json
-      contains: ['{"version": "6.0.1", "input_file": "genome.gbff.gz", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
+      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: 32aaf51315258af3b300d9a5bafd7bdc
@@ -26,75 +27,6 @@
     - path: output/antismash/test/regions.js
       contains: ['"seq_id": "NZ_CP069563.1"']
     - path: output/antismash/test/test.log
-      contains: ['antiSMASH version: 6.0.1']
+      contains: ["antiSMASH version: 6.0.1"]
     - path: output/antismash/versions.yml
       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/antismashlite
-    - antismash
-  files:
-    - path: output/antismash/clusterblast/stub_c.stub.txt
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/css/stub.css
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/images
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/js/stub.js
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/knownclusterblast/regionstub/ctg.stub.html
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/knownclusterblast/stub._c.stub.txt
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/svg/clusterblast.stub.svg
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/svg/knownclusterblast.stub.svg
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/stub.gbk
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/stub.json
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/stub.log
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/stub.zip
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/stub.region.stub.
-    - md5sum: d41d8cd98f00b204e9800998ecf8427egbk
-    - path: output/antismash/clusterblastoutpu
-    - md5sum: d41d8cd98f00b204e9800998ecf8427et.txt
-    - path: output/antismash/index.html
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/knownclusterblast
-    - md5sum: d41d8cd98f00b204e9800998ecf8427eoutput.txt
-    - path: output/antismash/regions.js
-    - md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: output/antismash/versions.yml
-      md5sum: 33e96b52f50beacd83c7e0feab8cb03b
-    - path: output/gunzip/genome.fna
-      md5sum: dafd38f5454b54fbea38245d773062a5
-    - 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
-      contains: ['NZ_CP069563.1']
-    - path: output/prokka/test/test.gff
-      md5sum: 9f733b702454e7750b7d4686369fe7e4
-    - path: output/prokka/test/test.log
-      contains: ["Annotation finished successfully."]
-    - path: output/prokka/test/test.sqn
-      contains: ['str "NZ_CP069563.1"']
-    - path: output/prokka/test/test.tbl
-      md5sum: 98f3b705f47b40255631ae43823e8271
-    - path: output/prokka/test/test.tsv
-      md5sum: 26e8aa4b2212f320e82b6db7c93d4461
-    - path: output/prokka/test/test.txt
-      md5sum: aea5834a64dff02d3588cecbe25c3914