- 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

Input parser

Closes #39

See merge request zavolan_group/pipelines/rnaseqpipeline!10

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

Fix params.direcionality for kallisto rule

See merge request zavolan_group/pipelines/rnaseqpipeline!9

Update fake samples file: tests/samples.tsv

See merge request zavolan_group/pipelines/rnaseqpipeline!7

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

Labkey api

See merge request zavolan_group/pipelines/rnaseqpipeline!8

BIOPZ-Börsch Anastasiya authored 5 years ago and Alex Kanitz committed 5 years ago

- add usage information in file `scripts/labkey_api.md`

Added sample fastq.gz paired-end input 1000 record files, adjusted dummy sample.tsv

See merge request zavolan_group/pipelines/rnaseqpipeline!6

add continuous integration support

See merge request zavolan_group/pipelines/rnaseqpipeline!5

Subpipelines

Closes #7, #8, #16, #17, #14, and #15

See merge request zavolan_group/pipelines/rnaseqpipeline!4

Rename snakemake/paired_end.snakemake to snakemake/paired_end.snakefile. Fix wiring of rules. Add fake tests.

Clean up unused code in snakemake/Snakefile. Add 2 threads in htseq_qa (paired end mode). Add example of tsv files from LabKey.

Merge branch 'subpipelines' of https://git.scicore.unibas.ch/zavolan_group/pipelines/rnaseqpipeline into subpipelines

Add script that generates heatmap and clustermap

See merge request zavolan_group/pipelines/rnaseqpipeline!3

Add script that performs PCA analysis

Closes #20

See merge request zavolan_group/pipelines/rnaseqpipeline!2