From 6a7aec8b41dc77d6c823e1a321208d58fc992427 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Thu, 5 May 2022 10:22:02 +0200 Subject: [PATCH] Remove prokka test workflow --- modules/antismash/antismashlite/main.nf | 27 ------- tests/modules/antismash/antismashlite/main.nf | 47 ------------ .../modules/antismash/antismashlite/test.yml | 74 +------------------ 3 files changed, 3 insertions(+), 145 deletions(-) diff --git a/modules/antismash/antismashlite/main.nf b/modules/antismash/antismashlite/main.nf index a4998be6..f6f8a30d 100644 --- a/modules/antismash/antismashlite/main.nf +++ b/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 - """ } diff --git a/tests/modules/antismash/antismashlite/main.nf b/tests/modules/antismash/antismashlite/main.nf index 2ef4430f..a625a0c1 100644 --- a/tests/modules/antismash/antismashlite/main.nf +++ b/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 ) -} diff --git a/tests/modules/antismash/antismashlite/test.yml b/tests/modules/antismash/antismashlite/test.yml index 96752b18..b1365414 100644 --- a/tests/modules/antismash/antismashlite/test.yml +++ b/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