mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Apply review suggestions + add stub for prokka test workflow
This commit is contained in:
jasmezz
parent
a992a0207e
commit
fa9f0753de
4 changed files with 97 additions and 42 deletions
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@ -22,22 +22,22 @@ process ANTISMASH_ANTISMASHLITE {
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output:
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tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
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tuple val(meta), path("$prefix/css/*.css") , emit: css_file
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tuple val(meta), path("$prefix/images") , emit: image_directory
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tuple val(meta), path("$prefix/js/*.js") , emit: javascript
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tuple val(meta), path("${prefix}/css/*.css") , emit: css_file
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tuple val(meta), path("${prefix}/images") , emit: image_directory
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tuple val(meta), path("${prefix}/js/*.js") , emit: javascript
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tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html
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tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt
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tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast
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tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast
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tuple val(meta), path("$prefix/*.gbk") , emit: gbk_input
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tuple val(meta), path("$prefix/*.json") , emit: json_results
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tuple val(meta), path("$prefix/*.log") , emit: log
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tuple val(meta), path("$prefix/*.zip") , emit: zip
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tuple val(meta), path("$prefix/*region*.gbk") , emit: gbk_results
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tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input
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tuple val(meta), path("${prefix}/*.json") , emit: json_results
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tuple val(meta), path("${prefix}/*.log") , emit: log
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tuple val(meta), path("${prefix}/*.zip") , emit: zip
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tuple val(meta), path("${prefix}/*region*.gbk") , emit: gbk_results
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tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput
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tuple val(meta), path("$prefix/index.html") , emit: html
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tuple val(meta), path("${prefix}/index.html") , emit: html
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tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput
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tuple val(meta), path("$prefix/regions.js") , emit: json_sideloading
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tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading
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path "versions.yml" , emit: versions
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when:
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@ -64,4 +64,31 @@ process ANTISMASH_ANTISMASHLITE {
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antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
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END_VERSIONS
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"""
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stub:
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"""
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mkdir ${prefix}
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touch ${prefix}/clusterblast/stub_c.stub.txt
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touch ${prefix}/css/stub.css
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touch ${prefix}/images
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touch ${prefix}/js/stub.js
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touch ${prefix}/knownclusterblast/regionstub/ctg.stub.html
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touch ${prefix}/knownclusterblast/stub._c.stub.txt
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touch ${prefix}/svg/clusterblast.stub.svg
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touch ${prefix}/svg/knownclusterblast.stub.svg
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touch ${prefix}/stub.gbk
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touch ${prefix}/stub.json
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touch ${prefix}/stub.log
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touch ${prefix}/stub.zip
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touch ${prefix}/stub.region.stub.gbk
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touch ${prefix}/clusterblastoutput.txt
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touch ${prefix}/index.html
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touch ${prefix}/knownclusterblastoutput.txt
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touch ${prefix}/regions.js
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
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END_VERSIONS
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"""
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}
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@ -87,11 +87,11 @@ output:
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pattern: "svg/knownclusterblast*.svg"
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- gbk_input:
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type: file
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description: Nucleotide sequence + annotations in GenBank file format; converted from input file
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description: Nucleotide sequence + annotations in GenBank format; converted from input file
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pattern: "*.gbk"
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- json_results:
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type: file
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description: Simple representation of all detected areas during the antiSMASH run in JSON format
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description: Nucleotide sequence + annotations in JSON format; converted from GenBank file (gbk_input)
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pattern: "*.json"
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- log:
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type: file
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@ -99,11 +99,11 @@ output:
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pattern: "*.log"
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- zip:
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type: file
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description: Contains a compressed version of the folder in zip format
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description: Contains a compressed version of the output folder in zip format
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pattern: "*.zip"
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- gbk_results:
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type: file
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description: Nucleotide sequence + annotations in GenBank file format; one file per antiSMASH hit
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description: Nucleotide sequence + annotations in GenBank format; one file per antiSMASH hit
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pattern: "*region*.gbk"
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- clusterblastoutput:
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type: file
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@ -10,6 +10,23 @@ include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/anti
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include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
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include { PROKKA } from '../../../modules/prokka/main.nf'
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process STUB_ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
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input:
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path database_css
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path database_detection
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path database_modules
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output:
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path("antismash_db") , emit: database
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path("antismash_dir"), emit: antismash_dir
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stub:
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"""
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mkdir antismash_db
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mkdir antismash_dir
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"""
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}
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workflow test_antismashlite {
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input_genome = [
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[ id:'test' ], // meta map
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@ -61,6 +78,6 @@ workflow test_prokka_antismashlite {
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UNTAR1 ( input_antismash_db1 )
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UNTAR2 ( input_antismash_db2 )
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UNTAR3 ( input_antismash_db3 )
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ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
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ANTISMASH_ANTISMASHLITE ( PROKKA.out.gbk, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir )
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STUB_ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
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ANTISMASH_ANTISMASHLITE ( PROKKA.out.gbk, STUB_ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, STUB_ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir )
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}
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@ -36,31 +36,42 @@
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- antismash/antismashlite
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- antismash
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files:
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- path: output/antismash/test/NZ_CP069563.1.region001.gbk
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contains: ['/tool="antismash"']
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- path: output/antismash/test/NZ_CP069563.1.region002.gbk
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contains: ['/tool="antismash"']
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- path: output/antismash/test/css/bacteria.css
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md5sum: 8b3c2f8b143d5245a5f42f55803c532c
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- path: output/antismash/test/index.html
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md5sum: 3773c3ec61fb1e8cd9a67791b37d9b79
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- path: output/antismash/test/js/antismash.js
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md5sum: 58e90c3d783ae014cc3d51849bcb50a2
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- path: output/antismash/test/js/jquery.js
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md5sum: 397754ba49e9e0cf4e7c190da78dda05
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- path: output/antismash/test/js/jquery.tablesorter.min.js
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md5sum: 5e9e08cef4d1be0eaa538e6eb28809a7
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- path: output/antismash/test/regions.js
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contains: [ '"seq_id": "NZ_CP069563.1"' ]
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- path: output/antismash/test/test.gbk
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contains: ['/tool="antismash"']
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- path: output/antismash/test/test.json
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contains: ['"id": "NZ_CP069563.1"']
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- path: output/antismash/test/test.log
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contains: ['antiSMASH status: SUCCESS']
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- path: output/antismash/test/test.zip
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- path: output/antismash/clusterblast/stub_c.stub.txt
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/css/stub.css
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/images
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/js/stub.js
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/knownclusterblast/regionstub/ctg.stub.html
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/knownclusterblast/stub._c.stub.txt
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/svg/clusterblast.stub.svg
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/svg/knownclusterblast.stub.svg
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/stub.gbk
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/stub.json
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/stub.log
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/stub.zip
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/stub.region.stub.
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- md5sum: d41d8cd98f00b204e9800998ecf8427egbk
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- path: output/antismash/clusterblastoutpu
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- md5sum: d41d8cd98f00b204e9800998ecf8427et.txt
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- path: output/antismash/index.html
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/knownclusterblast
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- md5sum: d41d8cd98f00b204e9800998ecf8427eoutput.txt
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- path: output/antismash/regions.js
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- md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/antismash/versions.yml
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md5sum: da6bed0032d0f7ad4741e0074ad6b1ff
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md5sum: 33e96b52f50beacd83c7e0feab8cb03b
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- path: output/gunzip/genome.fna
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md5sum: dafd38f5454b54fbea38245d773062a5
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- path: output/prokka/test/test.err
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@ -74,13 +85,13 @@
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- path: output/prokka/test/test.fsa
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md5sum: dbe7d3d43d46920802d2aec5cd177ddc
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- path: output/prokka/test/test.gbk
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md5sum: 286ea011a64c0d281de3981ed2f296ff
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contains: ['NZ_CP069563.1']
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- path: output/prokka/test/test.gff
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md5sum: 9f733b702454e7750b7d4686369fe7e4
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- path: output/prokka/test/test.log
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contains: ["Annotation finished successfully."]
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- path: output/prokka/test/test.sqn
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md5sum: a901ac190675f976e373219f0191d067
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contains: ['str "NZ_CP069563.1"']
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- path: output/prokka/test/test.tbl
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md5sum: 98f3b705f47b40255631ae43823e8271
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- path: output/prokka/test/test.tsv
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