Draft: Nftest migration metaphlan3 #8466
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nsang0u
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nsang0u
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famosab
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May 16, 2025
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We do not need this here as we have this defined globally :)
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| setup { | ||
| run("UNTAR") { | ||
| script "../../../untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.modules_testdata_base_path + 'delete_me/metaphlan_database.tar.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } |
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You can move the setup block out of the actual test to save some runs :)
| { assert path(process.out.biom[0][1]).text.contains('"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"') }, | ||
| { assert snapshot( | ||
| process.out.bt2out, | ||
| path(process.out.profile.get(0).get(1)).readLines()[2..-1] |
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Suggested change
| path(process.out.profile.get(0).get(1)).readLines()[2..-1] | |
| path(process.out.profile.get(0).get(1)).readLines()[2..-1].join('\n').md5() |
| { assert path(process.out.biom[0][1]).text.contains('"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"') }, | ||
| { assert snapshot( | ||
| process.out.bt2out, | ||
| path(process.out.profile.get(0).get(1)).readLines()[2..-1] |
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Suggested change
| path(process.out.profile.get(0).get(1)).readLines()[2..-1] | |
| path(process.out.profile.get(0).get(1)).readLines()[2..-1].join('\n').md5() |
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| setup { | ||
| run("UNTAR") { | ||
| script "../../../untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.modules_testdata_base_path + 'delete_me/metaphlan_database.tar.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } |
There was a problem hiding this comment.
Suggested change
| setup { | |
| run("UNTAR") { | |
| script "../../../untar/main.nf" | |
| process { | |
| """ | |
| input[0] = [ | |
| [ id:'test' ], | |
| file(params.modules_testdata_base_path + 'delete_me/metaphlan_database.tar.gz', checkIfExists: true) | |
| ] | |
| """ | |
| } | |
| } |
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| // [ | ||
| // [ | ||
| // [ | ||
| // [id:test, single_end:false], | ||
| // /Users/nnsangou/projects/nf-core/modules/.nf-test/tests/1b0b84df5ba4ed86ad76e5e202370d46/work/01/56a87b6f66c6ae | ||
| // bfee78b7301d0d0c/test_profile.txt | ||
| // ] | ||
| // ] | ||
| // ] |
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Suggested change
| // [ | |
| // [ | |
| // [ | |
| // [id:test, single_end:false], | |
| // /Users/nnsangou/projects/nf-core/modules/.nf-test/tests/1b0b84df5ba4ed86ad76e5e202370d46/work/01/56a87b6f66c6ae | |
| // bfee78b7301d0d0c/test_profile.txt | |
| // ] | |
| // ] | |
| // ] |
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| setup { | ||
| run("UNTAR") { | ||
| script "../../../untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.modules_testdata_base_path + 'delete_me/metaphlan_database.tar.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } |
There was a problem hiding this comment.
Suggested change
| setup { | |
| run("UNTAR") { | |
| script "../../../untar/main.nf" | |
| process { | |
| """ | |
| input[0] = [ | |
| [ id:'test' ], | |
| file(params.modules_testdata_base_path + 'delete_me/metaphlan_database.tar.gz', checkIfExists: true) | |
| ] | |
| """ | |
| } | |
| } | |
| } |
| { assert path(process.out.biom[0][1]).text.contains('"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"') }, | ||
| { assert snapshot( | ||
| process.out.bt2out, | ||
| path(process.out.profile.get(0).get(1)).readLines()[2..-1] |
There was a problem hiding this comment.
Suggested change
| path(process.out.profile.get(0).get(1)).readLines()[2..-1] | |
| path(process.out.profile.get(0).get(1)).readLines()[2..-1].join('\n').md5() |
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| // publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
|
|
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| // publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } |
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| withName: METAPHLAN3_METAPHLAN3 { | ||
| ext.args = '--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local' | ||
| } | ||
|
|
||
| withName: SAMTOOLS_VIEW { | ||
| ext.args = "--output-fmt sam" | ||
| } | ||
|
|
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Can you move these to the nf-test file itself? :)
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Closes #7621
Description of changes:
This PR migrates unit tests for metaphlan3/metaphlan3 from pytest to nf-test, and makes some minor corrections to these tests, described below.
params.modules_testdata_base_path