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.

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

- fixes some functions in `labkey_to_snakemake.py`
- add optional argument for trimming polyA tails; they are trimmed as follows:
  - if mate is sense, oligo-A is added to sample table for `cutadapt` rule to trim
  - if mate is antisense, oligo-T is added to sample table for `cutadapt` rule to trim
  - if option is set to `--trim_polya`, oligo-X stretch is added to sample table and `cutadapt` will not trim

- 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)

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

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