add ktimportkrona module #8859
add ktimportkrona module #8859
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| process KRONA_KTIMPORTKRONA { | |||
| label 'process_low' | |||
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Does your tool allow multi-threading? If yes you need to add the task.cpus somewhere, if no I would suggest to change this to process_single :)
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It doesn't. I'll do that, thx!
| 'biocontainers/krona:2.8.1--pl5321hdfd78af_1' }" | ||
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| input: | ||
| path html |
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Can we get a meta map here?
| path html | |
| tuple val(meta), path(html) |
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I followed the multiqc way here, since it does similar things - combining results of many (krona) processes into one. What's the standard here?
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Usually we hand a meta map with inputa and outputs (see any other modules). Not so sure why its different to multiqc. I am happy to accept as is, maybe we need to discuss this in the slack then :)
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I know that it's standard normally, but maybe the reason it's absent in multiqc is hidden in this sentence?
"Where applicable all sample-specific information e.g. 'id', 'single_end', 'read_group' MUST be provided as an input via a Groovy Map called 'meta'. This information may not be required in some instances, for example indexing reference genome files."
There are no sample-specific informations since there are multiple samples, so meta map isn't provided.
| path html | ||
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| output: | ||
| path "*.html" , emit: html |
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ? "-o ${task.ext.prefix}.html" : 'krona.krona.html' |
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| def prefix = task.ext.prefix ? "-o ${task.ext.prefix}.html" : 'krona.krona.html' | |
| def output = task.ext.prefix ? "${task.ext.prefix}.html" : 'krona.krona.html' |
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ? "-o ${task.ext.prefix}.html" : 'krona.krona.html' | ||
| """ | ||
| touch ${prefix} |
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| touch ${prefix} | |
| touch ${output} |
| setup { | ||
| run("KRAKENTOOLS_KREPORT2KRONA") { | ||
| script "../../../krakentools/kreport2krona/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [id: 'testreport'], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
| run("KRONA_KTIMPORTTEXT") { | ||
| script "../../ktimporttext/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = KRAKENTOOLS_KREPORT2KRONA.out.txt | ||
| """ | ||
| } | ||
| } | ||
| } |
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You can move the setup block out of the test block and reuse it along all tests :)
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Ahh good info! Thank you!
| { assert snapshot(process.out.versions).match() }, | ||
| { assert file(process.out.html[0]).text.contains('s__Severe_acute_respiratory_syndrome-related_coronavirus') }, | ||
| { assert file(process.out.html.get(0)).getText().contains("testreport") } |
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Ideally we want all the assertions to be reflected in the snapshot :) so we need to find a way to check for these things in the snapshot. I will link another modules to explain what I mean!
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Maybe it works to assert the whole output? Or is there a timestamp in the html file? Then we need to filter that out :)
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It's not a timestamp, the html outputs are just not consistent. Sometimes the colors are swapped and weird stuff like that :(
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ah ok then just go for my suggestion below :)
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thank you for your suggestions, applied the changes!
| { assert snapshot(process.out.versions).match() }, | ||
| { assert file(process.out.html[0]).text.contains('s__Severe_acute_respiratory_syndrome-related_coronavirus') }, | ||
| { assert file(process.out.html.get(0)).getText().contains("testreport1") }, | ||
| { assert file(process.out.html.get(0)).getText().contains("testreport2") } |
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| { assert snapshot(process.out.versions).match() }, | |
| { assert file(process.out.html[0]).text.contains('s__Severe_acute_respiratory_syndrome-related_coronavirus') }, | |
| { assert file(process.out.html.get(0)).getText().contains("testreport1") }, | |
| { assert file(process.out.html.get(0)).getText().contains("testreport2") } | |
| { assert snapshot( | |
| process.out.versions, | |
| path(process.out.html.get(0).get(1)).getText().contains("s__Severe_acute_respiratory_syndrome-related_coronavirus"), | |
| path(process.out.html.get(0).get(1)).getText().contains("testreport1"), | |
| path(process.out.html.get(0).get(1)).getText().contains("testreport2") | |
| ).match() }, |
PR checklist
Closes #7977
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile condaModule information:
Collect multiple krona reports in one file - kind of like multiqc, just for krona / classification files
https://manpages.ubuntu.com/manpages/jammy/man1/ktImportKrona.1.html
https://anaconda.org/bioconda/krona
https://github.com/marbl/Krona