[DO NOT MERGE] Test PR to see how the template would look like when creating a new modules #7430
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modules/nf-core/fastqc/meta.yml
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| description: raw_sequence file | ||
| pattern: "*.{fastq-like,sam,fastq,bam}" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/data_0848" |
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For each of these, it might be nice to have a comment saying which one they are for - makes it easier for people to copy and paste very common ones (fastq, fasta, bam etc)
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yes! it's planned, I forgot to implement it now 😄 thanks for the suggestion!
modules/nf-core/fastqc/main.nf
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| // TODO nf-core: List required Conda package(s). | ||
| // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). | ||
| // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. |
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This TODO should be in environment.yml?
| // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 | ||
| // If the software is unable to output a version number on the command-line then it can be manually specified | ||
| // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf | ||
| // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) |
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Could we explain how we do this when this is NOT possible?
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It is already explained, we mention it can be added manually. Would you rephrase it?
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Hmm, yes, it is on the line below, not sure why I said this, maybe I completely missed the following line.
We don't have great consistency where that VERSION string ends up in the file though, maybe it would be helpful to have it somewhere in the template.
modules/nf-core/fastqc/meta.yml
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| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - reads: | ||
| e.g. `[ id:'sample1', single_end:false ]` |
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Can we remove this from the template? It isn't often required and gets left and clutters things up.
| e.g. `[ id:'sample1', single_end:false ]` | |
| e.g. `[ id:'sample1]` |
modules/nf-core/fastqc/meta.yml
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| - "*.zip": | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - sequence_report: | ||
| # TODO nf-core: Update the information obtained form bio.tools and make sure that it is correct |
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| # TODO nf-core: Update the information obtained form bio.tools and make sure that it is correct | |
| # TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct |
Example for tools PR adding EDAM ontologies nf-core/tools#3418
The information from bio.tools is used to generate meta.yml and main.nf information when a module is created.