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

fix: Renamed samples_concat.tsv to samples.multiple_lanes.tsv. Renamed rows with split with the same name as the other test samples, so that I do not change the tests (md5 and sunch). Removed the one lane samples. Created config that uses this tsv file

BIOPZ-Katsantoni Maria authored 4 years ago and BIOPZ-Gypas Foivos committed 4 years ago

fix: added arguments for fragment size mean and sd required for the salmon quantification approach in single-end mode

- add 3 separate Conda environment files for installing
  - essential dependencies without Singularity (most users)
  - essential dependencies including Singularity (root users on Linux only)
  - non-essential dependencies (required for tests etc.)
- install Python dependencies via `pip` _within_ Conda environment to avoid #56
- update Conda-based installation instructions
  - describe usage of different environment files
  - add supported OS versions (macOS not yet added, because only installation works)
- update CI config to use same setup (based on Miniconda Docker image)

- 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

CJHerrmann authored 5 years ago and Alex Kanitz committed 5 years ago

- add script `tests/test_rule_graph/test.sh` to generate a rule graph in `images/rule_graph.svg`
- display rule graph created in `README.md` instead of specific workflow DAG
- add test script to GitLab CI config
- renamed test to create workflow DAG from `test_create_dag_chart` to `test_create_dag_image` (also output file is renamed from `images/workflow_dag.svg` to `images/dag_test_workflow.svg`

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

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

BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago

- replace corrupt input files
- add script that runs locally named `run_test.sh` in the snakemake directory
- add script to CI/CD pipeline
- fix typo in `paired_end.snakefile`
- update samples.tsv with fake adapter `XXXXXXX` when we do not want to trim them