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

- log and, if workflow is executed on cluster, cluster log directories are explicitly created in `Snakefile`
- location of main log directory can be configured in `config.yaml` (field `log_dir`, previously: `local_log`; requires change in script `labkey_to_snakemake.py` as well as subworkflows as field name is hard-coded there)
- location of cluster log directory can be configured in `cluster.json` (in field `__default__` -> `out`)
- `config.yaml` and `cluster.json` in `tests/input_files` are set such that a directory `logs/` is created in the directory where Snakemake is run (i.e., the directory of each test); cluster logs are stored in a subdirectory `logs/cluster`
- removes instructions to explicitly create log directories from docs and all test scripts
- cleans up main `Snakefile` (apart from Snakemake-specific syntax, now passes `flake8` linter test)

- 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

add tests to workflow integration test `tests/test_workflow_integration` that
- verify that STAR alignments match expected alignments (based on "ground truth" files)
- verify that Salmon gene quantification assign the correct number of reads to each gene (based on "ground truth files)

resolves #49

- replaces existing larger libraries and annotations in test cases `test_create_dag_chart` and `test_integration_workflow`
- adds the following new test files:
  - `chr1-10000-20000.fa`: artificial chromosome of length 10'000 (based on human chromosome 1)
  - `chr1-10000-20000.gtf`: matching gene annotation file with two gene and three multi-exon transcripts entries
  - `chr1-10000-20000.transcripts.fa`: sequences of the transcripts listed in the gene annotation file
  - `synthetic.mate_?.fastq.gz`: 10 read pairs randomly sampled from the genic regions of the artificial chromosome
  - `synthetic.*.bed`: BED files with expected alignments for each read; names of overlapping genes are specified in a 7th column
- updates file paths in the relevant sample tables
- extends and updates checksum checking of result files in CI/CD pipeline

`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)

- set up integration test for Snakefile in dedicated folder; current test case was left untouched for the time being, despite requiring large input files
- set up DAG chart creation test in dedicated folder; script creates an SVG representation of the workflow DAG at `images/workflow_dag.svg`
- both tests have been added to the GitLab CI/CD configuration; the latter test ensures that always the latest version of the
- all tests are now located inside subdirectories of `tests/`; test scripts and configuration files for test runs etc. have been moved to the appropriate test directories
- for the time being, required input files for each test are placed within the individual test directories; a layout for common test files should be introduced later and paths and bind paths in tests adapted
- make script `scripts/labkey_api.py` executable