- May 11, 2021
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- Apr 15, 2021
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- Feb 11, 2021
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- Jun 12, 2020
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Alex Kanitz authored
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- Apr 27, 2020
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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
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* Sequencing mode-related changes: * allowed sequencing modes in Snakemake input table changed from `paired_end` and `single_end` to `pe` and `se`, respectively * remove sequencing mode from output paths for each rule * corresponding wild cards removed entirely from all rules that do not depend on sequencing mode (currently all rules that are defined in the main `Snakefile` in the project root directory) * where absolutely necessary, sequencing mode is added as part of output file or directory instead * remove dependency of sequencing mode for rule for `FastQC`; now runs separately for each strand * Changes related to MultiQC and output file/directory structure * moving and renaming outputs for MultiQC is no longer required * code to create MultiQC custom config externalized into script `scripts/rhea_multiqc_config.py` * add MultiQC output files with deterministic output to md5 sum checks performed during execution of `tests/test_integration_workflow/test.{local,slurm}.sh` * output filenames for each rule now follow this general structure: `samples/{sample_name}/{rule}/{output_file}` * change log directory structure matches results directory structure * Miscellaneous changes * consistent, PEP8-compliant formatting in most parts, including Snakemake files, where allowed * remove rule `extract_decoys_salmon`; equivalent file `chrName.txt` produced by `star_index` is used instead * add rule `start` which copies sample data to the results directory and enforces uniform naming * refactoring of ALFA rules and modification of the CI/CD test to ensure compatibility
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