BIOPZ-Katsantoni Maria authored 5 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 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

- 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