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| // TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) | |||
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Remove the TODO statements everywhere (in meta.yml and modules/humann/main.nf)
| output: | ||
| // TODO nf-core: Named file extensions MUST be emitted for ALL output channels | ||
| tuple val(meta), path("outdir"), emit: outdir | ||
| // TODO nf-core: List additional required output channels/values here |
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Align the emit statements, e.g.:
tuple val(meta), path("outdir") , emit: outdir
path "versions.yml" , emit: versions
| // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) | ||
| """ | ||
| humann \\ | ||
| -o outdir \\ |
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I would suggest setting the outdir as a custom name per sample (e.g. ${prefix}_outdir). If you would use the module to analyze multiple samples in a pipeline, the results would overwrite each other. You should also change the output channel to: tuple val(meta), path("*_outdir"), emit: outdir if you were to do this.
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| name: "humann" | |||
| ## TODO nf-core: Add a description of the module and list keywords | |||
| description: write your description here | |||
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Don't forget to write a short description of the tool :p
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| input = [ | ||
| [ id:'mpa_v30_CHOCOPhlAn_201901' ], // meta map | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/qiaseq/SRR7545951-small_1.fastq.gz', checkIfExists: true), |
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I would suggest using the params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'] here instead of the full link. You can find all test datasets for modules either on https://github.com/nf-core/test-datasets/tree/modules or in the conf/test_data.config
| input = [ | ||
| [ id:'mpa_v30_CHOCOPhlAn_201901' ], // meta map | ||
| file('https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/qiaseq/SRR7545951-small_1.fastq.gz', checkIfExists: true), | ||
| file('chocophlan', checkIfExists: true), |
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What are these files meant to be?
| tags: | ||
| - humann | ||
| files: | ||
| - path: output/humann/versions.yml |
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Remove versions.yml from the file, if you update to the latest version of nf-core you won't have to delete these manually (you can also see that you are not getting any other output, is this supposed to happen?)
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| # | ||
| ## TODO nf-core: Delete / customise this example input |
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Update your input fields to correspond with the actual input of the module :)
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| ## TODO nf-core: Delete / customise this example output | ||
| - bam: |
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Also update your output field to correspond with the real output :)
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You can also see there are some trailing whitespaces detected by the |
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Hi @kohjy-ag , thank you for this PR! We are merging as many modules as possible now due to and impending restructuring of the entire repo. This will mean you will need to update the module to reflect these changes before it can be merged in the future. It appears like this module isn't ready to be merged so we are converting it to draft and adding the WIP label. If this isn't the case please let us know and we will try to get the module in before the changes. Thanks again! |
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Hi there! We've noticed there hasn't been much activity here. Are you still planning on working on this? Cheers |
5 participants
PR checklist
Closes #XXX
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware