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Alex Kanitz authored
- clean up command line interface - improve descriptions - add consistent structure - remove or merge superfluous CLI arguments - set defaults - update test calls - update docs - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table - allow user to specify environment variables and relative paths in input table and on CLI - relative paths in the input table are interpreted with respect to the directory containing the input table - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown - set STAR index size to read length - 1 - remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly - rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly - add logging - add docstrings to module and all functions - add typing definitions to all functions - restructure and comment code to improve readability - linters `flake8` and `mypy` pass
Alex Kanitz authored- clean up command line interface - improve descriptions - add consistent structure - remove or merge superfluous CLI arguments - set defaults - update test calls - update docs - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table - allow user to specify environment variables and relative paths in input table and on CLI - relative paths in the input table are interpreted with respect to the directory containing the input table - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown - set STAR index size to read length - 1 - remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly - rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly - add logging - add docstrings to module and all functions - add typing definitions to all functions - restructure and comment code to improve readability - linters `flake8` and `mypy` pass
config.yaml 412 B
---
samples: "../input_files/samples.tsv"
output_dir: "results"
log_dir: "logs"
kallisto_indexes: "results/kallisto_indexes"
salmon_indexes: "results/salmon_indexes"
star_indexes: "results/star_indexes"
alfa_indexes: "results/alfa_indexes"
report_description: "No description provided by user"
report_logo: "../../images/logo.128px.png"
report_url: "https://zavolan.biozentrum.unibas.ch/"
...