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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -4,4 +4,4 @@ channels: | |
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - bioconda::antismash-lite=6.1.1 | ||
| - bioconda::antismash-lite=7.1.0 | ||
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126 changes: 126 additions & 0 deletions
126
modules/nf-core/antismash/antismashlite/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,126 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process ANTISMASH_ANTISMASHLITE" | ||
| script "../main.nf" | ||
| process "ANTISMASH_ANTISMASHLITE" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "antismash" | ||
| tag "antismash/antismashlite" | ||
| tag "antismash/antismashlitedownloaddatabases" | ||
| tag "gunzip" | ||
| tag "untar" | ||
|
|
||
| setup { | ||
| run("UNTAR", alias: "UNTAR_CSS") { | ||
| script "modules/nf-core/untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ ], | ||
| file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| run("UNTAR", alias: "UNTAR_DETECTION") { | ||
| script "modules/nf-core/untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ ], | ||
| file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| run("UNTAR", alias: "UNTAR_MODULES") { | ||
| script "modules/nf-core/untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ ], | ||
| file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| run("ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES") { | ||
| script "modules/nf-core/antismash/antismashlitedownloaddatabases" | ||
| process { | ||
| """ | ||
| input[0] = UNTAR_CSS.out.untar.map{ it[1] } | ||
| input[1] = UNTAR_DETECTION.out.untar.map{ it[1] } | ||
| input[2] = UNTAR_MODULES.out.untar.map{ it[1] } | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| run("GUNZIP") { | ||
| script "modules/nf-core/gunzip/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("antismashlite - bacteroides_fragilis - genome") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = GUNZIP.out.gunzip | ||
| input[1] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database | ||
| input[2] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir | ||
| input[3] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert path(process.out.gbk_results.get(0).get(1).get(0)).text.contains("##antiSMASH-Data-START##") }, | ||
| { assert snapshot(process.out.html_accessory_files).match("html_accessory_files") }, | ||
| { assert path(process.out.gbk_input.get(0).get(1).get(0)).text.contains("##antiSMASH-Data-END##") }, | ||
| { assert path(process.out.zip.get(0).get(1)).exists() }, | ||
| { assert path(process.out.html.get(0).get(1)).text.contains("https://antismash.secondarymetabolites.org/") }, | ||
| { assert path(process.out.json_sideloading.get(0).get(1)).text.contains("\"seq_id\": \"NZ_CP069563.1\"") }, | ||
| { assert path(process.out.log.get(0).get(1)).text.contains("antiSMASH status: SUCCESS") }, | ||
| { assert snapshot(process.out.versions).match("versions") } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("antismashlite - bacteroides_fragilis - genome - stub") { | ||
|
|
||
| options "-stub" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = GUNZIP.out.gunzip | ||
| input[1] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database | ||
| input[2] = ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir | ||
| input[3] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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