- 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

BIOPZ-Katsantoni Maria authored 4 years ago and Alex Kanitz committed 4 years ago

* 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

BIOPZ-Katsantoni Maria authored 4 years ago and Alex Kanitz committed 4 years ago

In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya
feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt
depending on which is the sense or antisense mate the appropriate variable is populated
and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by
cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.

- 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>

BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago

- 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

BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago

- separate organism genome architecture (different input folder)
- change MD5 checksums to match the new output

`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)

BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago

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