Formatting custom SAM header #21
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Formatting custom SAM header
This PR is against the
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fixed base from main to dev |
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(tip: when you create a PR, you can add some text like "Closes #9" or select the issue in the "Development" menu on the right-hand side. That'll update the board automatically and move the issue to "In progress" and "Done") |
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Good tip! I was wondering why it didn't update the board...
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muffato
reviewed
Jun 27, 2024
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That looks good and clean. I've got these comments:
- You're calling
PREPARE_HEADERtwice, once on each.dictfile. But the.dictfiles only differ because theirURfield point to separate Fasta files, and after you've editedURas per the "SOURCE", they become identical. We can probably just compute the header once ? - The "SOURCE" that you write down in the
URfield is the path of the directory on the NCBI FTP. I think it should rather be a path to the file. - Finally, I think we should un-publish the samtools dict file because the new header is a richer version of it
The only reason for this was that I was worried that in the case of any hard-masking the checksum values written to the dict files could differ? If we know that only soft-masking will ever be run than I don't think that should be possible though |
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Ok all issues dealt with -- removed the 2nd reheader call as I realised the checksums will always be identical between the two. Ready for review! |
muffato
reviewed
Jun 27, 2024
Co-authored-by: Matthieu Muffato <[email protected]>
muffato
approved these changes
Jul 4, 2024
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Closes #9
Added new sub workflow which formats a new output file *.header.sam containing the metadata items requested in #9.
The new file contains the ftp source URL (UR:), species name (SP:), GCA accession (AS:), and alternate name (AN:) taken from the Assigned-Molecule column in the assembly/{genome}.assembly_report.txt files.
Other changes:
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).