mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
Remove prokka test workflow
This commit is contained in:
jasmezz
parent
480c4ced78
commit
6a7aec8b41
3 changed files with 3 additions and 145 deletions
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@ -64,31 +64,4 @@ 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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@ -2,30 +2,11 @@
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nextflow.enable.dsl = 2
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include { GUNZIP } from '../../../modules/gunzip/main.nf'
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include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
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include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
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include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
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include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
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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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@ -53,31 +34,3 @@ workflow test_antismashlite {
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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 ( input_genome, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir )
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}
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workflow test_prokka_antismashlite {
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input_gunzip = [ [ id:'test' ], // meta map
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file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]
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input_antismash_db1 = [
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[],
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
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]
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input_antismash_db2 = [
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[],
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
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]
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input_antismash_db3 = [
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[],
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
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]
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GUNZIP ( input_gunzip )
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PROKKA ( GUNZIP.out.gunzip, [], [] )
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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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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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@ -13,7 +13,8 @@
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- path: output/antismash/test/genome.gbk
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contains: ['/tool="antismash"']
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- path: output/antismash/test/genome.json
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contains: ['{"version": "6.0.1", "input_file": "genome.gbff.gz", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
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contains:
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['{"version": "6.0.1", "input_file": "genome.gbff.gz", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
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- path: output/antismash/test/genome.zip
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- path: output/antismash/test/index.html
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md5sum: 32aaf51315258af3b300d9a5bafd7bdc
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@ -26,75 +27,6 @@
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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.log
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contains: ['antiSMASH version: 6.0.1']
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contains: ["antiSMASH version: 6.0.1"]
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- path: output/antismash/versions.yml
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md5sum: 759431a43da33e2ef8e2d0ebd79a439b
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- name: antismash antismashlite test_prokka_antismashlite
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command: nextflow run tests/modules/antismash/antismashlite -entry test_prokka_antismashlite -c tests/config/nextflow.config
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tags:
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- antismash/antismashlite
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- antismash
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files:
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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: 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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md5sum: 194fd8a1d1cde9919841a1afd4414760
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- path: output/prokka/test/test.faa
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md5sum: 8fefbfa7860f280cc881c3a3b377d6da
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- path: output/prokka/test/test.ffn
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md5sum: 9c4d4d7dc28625bcb13c6fbd27ca13c3
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- path: output/prokka/test/test.fna
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md5sum: 96aa7707b864499745e8946f169ae8e0
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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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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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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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md5sum: 26e8aa4b2212f320e82b6db7c93d4461
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- path: output/prokka/test/test.txt
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md5sum: aea5834a64dff02d3588cecbe25c3914
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