- 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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- Feb 18, 2020
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Alex Kanitz authored
- trap call functionalized through cleanup() function - function added to all test scripts - function prints out exit status of last command before trap - flag `--verbose` added to Snakemake calls in all test scripts - script tests rename to follow naming convention 'test_script_<script_name>_<script_run_mode>
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- Feb 15, 2020
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- add script that prepares Snakemake input files 'samples.tsv' and 'config.yaml' from LabKey table - script either connects to API directly (with '--remote' and related options) or processes a tab-separated LabKey dump file - add tests for both use cases - common input files for tests now in 'tests/input_files' - update all other tests to account for new file locations - update documentation
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- Feb 14, 2020
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Alex Kanitz authored
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- separate organism genome architecture (different input folder) - change MD5 checksums to match the new output
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- Feb 07, 2020
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- Feb 04, 2020
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Alex Kanitz authored
`README.md` file describes - aim and background of the project (including the workflow DAG representation) - how to install requirements (including setting up a `conda` environment for the project) - how to execute the workflow run integration test - how to run the workflow on your own samples (including how to auto-generate required params from LabKey metadata) Additional minor changes: - minor changes in various test and related files, including updates of paths - root directory now includes subdirectory `runs/` for a user's workflow runs (contents not version-controlled)
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- Feb 03, 2020
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Adds script `scripts/labkey_to_snakemake.py` which - maps LabKey table fields to Snakemake parameters - assembles required parameters from the table data - infers required parameters from the input data - produces files `config.yaml` and `samples.tsv` required by the Snakemake pipeline A self-contained integration test for the script is located at `tests/test_scripts_labkey_to_snakemake` (execute script `test.sh`) and was added to the CI/CD pipeline. Note that intermittent changes to the `master` branch were merged into this branch to forego conflicts during merging. Closes #39
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