- Mar 20, 2020
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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.
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- Mar 19, 2020
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- Mar 18, 2020
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- Mar 17, 2020
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- Mar 13, 2020
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BIOPZ-Katsantoni Maria authored
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- Mar 12, 2020
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Dominik Burri authored
- 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
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- Mar 06, 2020
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BIOPZ-Gypas Foivos authored
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.
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- Feb 21, 2020
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Alex Kanitz authored
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- 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
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- Feb 20, 2020
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Alex Kanitz authored
- 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)
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- Feb 17, 2020
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- add rule for input preparation (GTF to BED12) - add rule for TIN score calculation - update rule graph and DAG image - update Slurm cluster config
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- Feb 14, 2020
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Alex Kanitz authored
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- Feb 08, 2020
- Feb 07, 2020
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Alex Kanitz authored
- 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
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- Jan 24, 2020
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BIOPZ-Gypas Foivos authored
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- 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
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- Dec 20, 2019
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BIOPZ-Gypas Foivos authored
Rename snakemake/paired_end.snakemake to snakemake/paired_end.snakefile. Fix wiring of rules. Add fake tests.
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BIOPZ-Gypas Foivos authored
Clean up unused code in snakemake/Snakefile. Add 2 threads in htseq_qa (paired end mode). Add example of tsv files from LabKey.
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BIOPZ-Gypas Foivos authored
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BIOPZ-Katsantoni Maria authored
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