Skip to content

Fix KrakenUniq classified reads output format mismatch #489

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 5 commits into from
May 21, 2024
Merged

Fix KrakenUniq classified reads output format mismatch #489

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
c3b624a
Install new module and start extracting seq type
jfy133 May 16, 2024
1978649
Merge branch 'dev' into ku-fix
jfy133 May 16, 2024
faa002d
Fix metadata
jfy133 May 16, 2024
ad008c8
Ensure to published FASTQ files too
jfy133 May 16, 2024
d5d82b1
Apply suggestions from code review
jfy133 May 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,7 @@ process {
publishDir = [
path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt,fasta.gz}'
pattern: '*.{txt,fastq.gz,fasta.gz}'
]
}

Expand Down
4 changes: 2 additions & 2 deletions docs/output.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -398,8 +398,8 @@ You will only receive the `.fastq` and `*classifiedreads.txt` file if you supply

- `krakenuniq/`
- `<db_name>/`
- `<sample_id>_<db_name>[.merged].classified.fasta.gz`: Optional FASTA file containing all reads that had a hit against a reference in the database for a given sample. Paired-end input reads are merged in this output.
- `<sample_id>_<db_name>[.merged].unclassified.fasta.gz`: Optional FASTA file containing all reads that did not have a hit in the database for a given sample. Paired-end input reads are merged in this output.
- `<sample_id>_<db_name>[.merged].classified.fast{a,q}.gz`: Optional FASTA file containing all reads that had a hit against a reference in the database for a given sample. Paired-end input reads are merged in this output.
- `<sample_id>_<db_name>[.merged].unclassified.fast{a,q}.gz`: Optional FASTA file containing all reads that did not have a hit in the database for a given sample. Paired-end input reads are merged in this output.
- `<sample_id>_<db_name>.krakenuniq.report.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits.
- `<sample_id>_<db_name>.krakenuniq.classified.txt`: An optional list of read IDs and the hits each read had against each database for a given sample.

Expand Down
2 changes: 1 addition & 1 deletion modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@
},
"krakenuniq/preloadedkrakenuniq": {
"branch": "master",
"git_sha": "8bbaa881ab9e59f3e18680550d65d52339640630",
"git_sha": "9de9365c3ca6071ec01705919f6667c718ef47b4",
"installed_by": ["modules"]
},
"krona/ktimporttaxonomy": {
Expand Down
59 changes: 32 additions & 27 deletions modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

30 changes: 18 additions & 12 deletions modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading