Skip to content

feat(cli): add short single-dash aliases for options and bump to v1.1.1 #20

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
iliapopov17 merged 3 commits into from
Jun 2, 2026
Merged

feat(cli): add short single-dash aliases for options and bump to v1.1.1 #20

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
733fc9e
feat(cli): add short single-dash aliases for domain and overwrite flags
iliapopov17 Jun 2, 2026
65fae17
docs(readme): update CLI help usage with new single-dash aliases
iliapopov17 Jun 2, 2026
c3f370e
chore(release): bump version to 1.1.1
iliapopov17 Jun 2, 2026
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
40 changes: 21 additions & 19 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69,24 +69,26 @@ Usage: KrakenParser [OPTIONS] COMMAND [ARGS]...
to see options for a specific step.

╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --input -i PATH Directory containing Kraken2 report files. │
│ --output -o PATH Output directory. │
│ --viruses Extract only VIRUSES domain taxa in the │
│ pipeline. │
│ --bacteria Extract only BACTERIA domain taxa in the │
│ pipeline. │
│ --fungi Extract only FUNGI kingdom taxa in the │
│ pipeline. │
│ --archaea Extract only ARCHAEA domain taxa in the │
│ pipeline. │
│ --keep-human Do not filter human-related taxa. │
│ --version -V Show version and exit. │
│ --depth -d INTEGER Rarefaction depth for β-diversity. │
│ [default: 1000] │
│ --seed -s INTEGER Random seed for reproducible rarefaction. │
│ --overwrite Overwrite the output directory if it already │
│ exists. │
│ --help -h Show this message and exit. │
│ --input -i PATH Directory containing Kraken2 report │
│ files. │
│ --output -o PATH Output directory. │
│ --viruses -viruses Extract only VIRUSES domain taxa in │
│ the pipeline. │
│ --bacteria -bacteria Extract only BACTERIA domain taxa in │
│ the pipeline. │
│ --fungi -fungi Extract only FUNGI kingdom taxa in │
│ the pipeline. │
│ --archaea -archaea Extract only ARCHAEA domain taxa in │
│ the pipeline. │
│ --keep-human -keep-human Do not filter human-related taxa. │
│ --version -V Show version and exit. │
│ --depth -d INTEGER Rarefaction depth for β-diversity. │
│ [default: 1000] │
│ --seed -s INTEGER Random seed for reproducible │
│ rarefaction. │
│ --overwrite -overwrite Overwrite the output directory if it │
│ already exists. │
│ --help -h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Advanced (Step-by-step pipeline control) ───────────────────────────────────╮
│ mpa Convert a Kraken2 report to MetaPhlAn (MPA) format. │
Expand Down Expand Up @@ -319,7 +321,7 @@ results/
│ ├─ counts_genus.txt
│ ├─ ...
│ └─ counts_phylum.txt
└─ krakenparser.log # Pipeline execution logs
└─ krakenparser.log # Pipeline execution logs
```

## Conclusion
Expand Down
23 changes: 18 additions & 5 deletions krakenparser/krakenparser.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,19 +60,31 @@ def main_callback(
None, "-o", "--output", help="Output directory."
),
viruses: bool = typer.Option(
False, "--viruses", help="Extract only VIRUSES domain taxa in the pipeline."
False,
"-viruses",
"--viruses",
help="Extract only VIRUSES domain taxa in the pipeline.",
),
bacteria: bool = typer.Option(
False, "--bacteria", help="Extract only BACTERIA domain taxa in the pipeline."
False,
"-bacteria",
"--bacteria",
help="Extract only BACTERIA domain taxa in the pipeline.",
),
fungi: bool = typer.Option(
False, "--fungi", help="Extract only FUNGI kingdom taxa in the pipeline."
False,
"-fungi",
"--fungi",
help="Extract only FUNGI kingdom taxa in the pipeline.",
),
archaea: bool = typer.Option(
False, "--archaea", help="Extract only ARCHAEA domain taxa in the pipeline."
False,
"-archaea",
"--archaea",
help="Extract only ARCHAEA domain taxa in the pipeline.",
),
keep_human: bool = typer.Option(
False, "--keep-human", help="Do not filter human-related taxa."
False, "-keep-human", "--keep-human", help="Do not filter human-related taxa."
),
version: Optional[bool] = typer.Option(
None,
Expand All @@ -90,6 +102,7 @@ def main_callback(
),
overwrite: bool = typer.Option(
False,
"-overwrite",
"--overwrite",
help="Overwrite the output directory if it already exists.",
),
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

[project]
name = "krakenparser"
version = "1.1.0"
version = "1.1.1"
description = "A collection of scripts designed to process Kraken2 reports and convert them into CSV format."
readme = {file = "README.md", content-type = "text/markdown"}
license = {file = "LICENSE"}
Expand Down
Loading