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.

- renaming bedgraph
- creating ALFA qc plots

removed conda dependence, moved import statement.

included ALFA in finish rule, corrected annotation.gtf and config.yaml, created new .svg

Merged paired end and single end rules for star_rpm and index_genomic_alignment_samtools. Fixed wiring of calculate tin score: bam should be input and not params.

BIOPZ-Iborra de Toledo Paula authored 5 years ago and Alex Kanitz committed 5 years ago

-  Remove files with non-deterministic output from `tests/test_integration_workflow/expected_output.files`
-  Update MD5 sums in `tests/test_integration_workflow/expected_output.md5`
-  Update new workflow DAG and rule graph images

- 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-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago

- add rule for input preparation (GTF to BED12)
- add rule for TIN score calculation
- update rule graph and DAG image
- update Slurm cluster config

BIOPZ-Iborra de Toledo Paula authored 5 years ago and Alex Kanitz committed 5 years ago

- Rules now integrated include #7, #8, #9, #10, #11, #12, #13, #14, #15, #16, #17
- Applies both for single-end and paired-end subworkflows
- DAG image updated
- Test sample tables and outcomes updated
- Unused preprocessing subworkflow removed

Closes #48
Closes #6

- remove log files and add '.snakemake' directories to '.gitignore'
- update wrong link in 'README.md'
- delete superfluous script documentation 'scripts/labkey_api.md'
- add Snakemake-specific file extension '.smk' to subworkflows
- remove non-deterministic workflow output from md5 sums

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

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.