Update RTN/TNI module #8500
Update RTN/TNI module #8500
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Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
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| process RTN_TNA { | |||
| debug true | |||
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You probably need to remove this?
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| input: | ||
| tuple val(meta), path(tni_object) | ||
| tuple val(meta), path(degs) |
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I think that the best practice is to give a different name such as meta2, meta3, etc. because you can't guarantee that all metadata channels will be identical.
| writeLines( | ||
| c( | ||
| '"${task.process}":', | ||
| paste(' bioconductor-rtn:', rtn.version) |
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How about also outputting R's version?
| def DEGs = file("${workDir}/degs.tsv") | ||
| DEGs.text = content | ||
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| run("RTN_TNI") { |
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You can also save the output of the rtn/tni package on https://github.com/nf-core/test-datasets/, to avoid running it twice (since it is already ran in its own test suite).
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Just add config './nextflow.config next to e.g. the tags or just inside the when block next to the e.g. options
| { assert file(process.out.gsea1_plot[0][1]).exists() }, | ||
| { assert file(process.out.gsea2_object[0][1]).exists() }, | ||
| { assert file(process.out.gsea2_plot[0][1]).exists() }, | ||
| { assert file(process.out.versions[0]).exists() } |
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For this one and the other outputs that have no randomness inside, can you make stronger tests such as assert snapshot(process.out.versions).match() ?
| ################################################ | ||
| ################################################ | ||
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| tni_object <- readRDS('tni.rds') |
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What if tni_object has a different name?
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| process { | |||
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I do not see this file (nor nextflow.config3 being used).
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Instead of using the nonstandard config{2,3,4} notation, you could instead use Mahesh's clever system of params: https://nf-co.re/docs/guidelines/components/modules#configuration-of-extargs-in-tests
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| process { | |||
| withName: RTN_TNI { | |||
| ext.args = '--tfs ENSG00000125798,ENSG00000125816' | |||
| ext.args = '--n_permutations 12' | |||
PR checklist
Closes #XXX
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 conda