Add sylph/profile module #7118
Add sylph/profile module #7118
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| description: | | ||
| List of input FastQ/FASTA files of size 1 and 2 for single-end and paired-end data, | ||
| respectively. They are automatically sketched to .sylsp/.syldb | ||
| - - pre_sketched_files: |
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This says a Presketched db, but your test input supplies a fasta file.
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The documentation says:
Pre-sketched *.syldb/*.sylsp files. Raw single-end fastq/fasta are allowed and will be automatically sketched to .sylsp/.syldb.
That is why I supplied a fasta file. Updated the meta.yml file with this info too.
| "versions.yml:md5,7b5a545483277cc0ff9189f8891e737f" | ||
| ], | ||
| [ | ||
| false |
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Is it expected that the contains check always leads to the string not being contained?
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The string should be contained. Looking into it.
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.versions, | ||
| process.out.profile_out.collect { file(it[1]).readLines().contains("complete genome") }, |
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MAybe you can assert the file a bit better using: https://github.com/lukfor/nft-csv
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Do you mean to count the columns of the output file?
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anything that makes sense - counting columns or asserting column header both seems fine to me
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@sofstam , do you need a hand to get this finished off? |
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@SPPearce Was on holidays, looking at the comments now :) |
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
PR checklist
Moves the local module
sylph/profileto nf-core modules. Closes nf-core/seqinspector#65Removes unnecessary pattern from
sylph/sketchmeta file.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