diff --git a/modules/antismash/antismashlite/main.nf b/modules/antismash/antismashlite/main.nf index c92f983e..a4998be6 100644 --- a/modules/antismash/antismashlite/main.nf +++ b/modules/antismash/antismashlite/main.nf @@ -22,22 +22,22 @@ process ANTISMASH_ANTISMASHLITE { output: tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file - tuple val(meta), path("$prefix/css/*.css") , emit: css_file - tuple val(meta), path("$prefix/images") , emit: image_directory - tuple val(meta), path("$prefix/js/*.js") , emit: javascript + tuple val(meta), path("${prefix}/css/*.css") , emit: css_file + tuple val(meta), path("${prefix}/images") , emit: image_directory + tuple val(meta), path("${prefix}/js/*.js") , emit: javascript tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast - tuple val(meta), path("$prefix/*.gbk") , emit: gbk_input - tuple val(meta), path("$prefix/*.json") , emit: json_results - tuple val(meta), path("$prefix/*.log") , emit: log - tuple val(meta), path("$prefix/*.zip") , emit: zip - tuple val(meta), path("$prefix/*region*.gbk") , emit: gbk_results + tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input + tuple val(meta), path("${prefix}/*.json") , emit: json_results + tuple val(meta), path("${prefix}/*.log") , emit: log + tuple val(meta), path("${prefix}/*.zip") , emit: zip + tuple val(meta), path("${prefix}/*region*.gbk") , emit: gbk_results tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput - tuple val(meta), path("$prefix/index.html") , emit: html + tuple val(meta), path("${prefix}/index.html") , emit: html tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput - tuple val(meta), path("$prefix/regions.js") , emit: json_sideloading + tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading path "versions.yml" , emit: versions when: @@ -64,4 +64,31 @@ 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 + """ } diff --git a/modules/antismash/antismashlite/meta.yml b/modules/antismash/antismashlite/meta.yml index d726ad3e..22056202 100644 --- a/modules/antismash/antismashlite/meta.yml +++ b/modules/antismash/antismashlite/meta.yml @@ -87,11 +87,11 @@ output: pattern: "svg/knownclusterblast*.svg" - gbk_input: type: file - description: Nucleotide sequence + annotations in GenBank file format; converted from input file + description: Nucleotide sequence + annotations in GenBank format; converted from input file pattern: "*.gbk" - json_results: type: file - description: Simple representation of all detected areas during the antiSMASH run in JSON format + description: Nucleotide sequence + annotations in JSON format; converted from GenBank file (gbk_input) pattern: "*.json" - log: type: file @@ -99,11 +99,11 @@ output: pattern: "*.log" - zip: type: file - description: Contains a compressed version of the folder in zip format + description: Contains a compressed version of the output folder in zip format pattern: "*.zip" - gbk_results: type: file - description: Nucleotide sequence + annotations in GenBank file format; one file per antiSMASH hit + description: Nucleotide sequence + annotations in GenBank format; one file per antiSMASH hit pattern: "*region*.gbk" - clusterblastoutput: type: file diff --git a/tests/modules/antismash/antismashlite/main.nf b/tests/modules/antismash/antismashlite/main.nf index 3044250a..2ef4430f 100644 --- a/tests/modules/antismash/antismashlite/main.nf +++ b/tests/modules/antismash/antismashlite/main.nf @@ -10,6 +10,23 @@ include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/anti 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 = [ [ id:'test' ], // meta map @@ -61,6 +78,6 @@ workflow test_prokka_antismashlite { 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 ( PROKKA.out.gbk, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir ) + 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 ) } diff --git a/tests/modules/antismash/antismashlite/test.yml b/tests/modules/antismash/antismashlite/test.yml index a2adad79..96752b18 100644 --- a/tests/modules/antismash/antismashlite/test.yml +++ b/tests/modules/antismash/antismashlite/test.yml @@ -36,31 +36,42 @@ - antismash/antismashlite - antismash 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/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: da6bed0032d0f7ad4741e0074ad6b1ff + md5sum: 33e96b52f50beacd83c7e0feab8cb03b - path: output/gunzip/genome.fna md5sum: dafd38f5454b54fbea38245d773062a5 - path: output/prokka/test/test.err @@ -74,13 +85,13 @@ - path: output/prokka/test/test.fsa md5sum: dbe7d3d43d46920802d2aec5cd177ddc - path: output/prokka/test/test.gbk - md5sum: 286ea011a64c0d281de3981ed2f296ff + 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 - md5sum: a901ac190675f976e373219f0191d067 + contains: ['str "NZ_CP069563.1"'] - path: output/prokka/test/test.tbl md5sum: 98f3b705f47b40255631ae43823e8271 - path: output/prokka/test/test.tsv