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Adjusted handling of compressed tar archive containing kraken2 database #54

Merged
merged 2 commits into from
Jun 23, 2020
Merged

Adjusted handling of compressed tar archive containing kraken2 database #54

merged 2 commits into from
Jun 23, 2020

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skrakau
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@skrakau skrakau commented Jun 22, 2020

Adjusted handling of the compressed tar archive file containing the kraken2 database in the process kraken2_db_preparation. So far it was assumed that the name of the contained folder within the tar archive equals the base name of the compressed tar archive file. For the provided MiniKraken2 database this is not always the case, i.e. sometimes only a prefix matches but without a consistent pattern (see also https://ccb.jhu.edu/software/kraken2/index.shtml?t=downloads).
Since I did not want to make any further assumptions on the folder name, I changed this to use all *.k2d in any contained folder, assuming each provided db file contains exactly one folder with *.k2d files.

Additionally I updated the links in the help and documentation to the minikraken2 database, which was recently updated.

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md

@skrakau skrakau requested a review from d4straub June 22, 2020 18:00
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d4straub approved these changes Jun 23, 2020
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Seems good!

@skrakau skrakau merged commit 748c779 into nf-core:dev Jun 23, 2020
@d4straub d4straub mentioned this pull request Jul 15, 2020
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@d4straub d4straub mentioned this pull request Sep 10, 2020
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@skrakau skrakau mentioned this pull request Sep 10, 2020
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@skrakau skrakau deleted the fix_db_name branch November 4, 2020 10:30
@alirizaaribas-ibg
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Hello,
I have a fully downloaded version of kraken2db in my local hpc. How can I set kraken2db parameter for mag, not the minidb? I see no other explanation in parameter docs.
Thanks.

--kraken2_db
Database for taxonomic binning with kraken2.

E.g. "ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz".

@skrakau
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skrakau commented Mar 5, 2021

Hi @alirizaaribas-ibg,
you should be able to set it with --kraken2_db. It has to be a tar.gz file though and must contain *.k2d files.
You can open a new issue, if there a still problems.

@alirizaaribas-ibg
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I compressed our kraken2db into a tar.gz with k2d files. Krona_db step gave checksum error. How can I understand this error is related with my compressed file? Thanks.

image

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