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  1. Mar 20, 2020
    • BIOPZ-Katsantoni Maria's avatar
      Fix Poly(A)-trimming rule · 392b04d2
      BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed
      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.
      392b04d2
  2. Mar 19, 2020
  3. Mar 18, 2020
  4. Mar 17, 2020
  5. Mar 13, 2020
  6. Mar 12, 2020
    • Dominik Burri's avatar
      added rule for · 37fb0fd0
      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
      37fb0fd0
  7. Mar 06, 2020
  8. Feb 21, 2020
  9. Feb 20, 2020
    • Alex Kanitz's avatar
      create log directories in Snakefile\ · 5e1ec85e
      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)
      5e1ec85e
  10. Feb 17, 2020
    • BIOPZ-Bak Maciej's avatar
      add TIN score calculation · c538fe8b
      BIOPZ-Bak Maciej authored and Alex Kanitz's avatar Alex Kanitz committed
      - add rule for input preparation (GTF to BED12)
      - add rule for TIN score calculation
      - update rule graph and DAG image
      - update Slurm cluster config
      c538fe8b
  11. Feb 14, 2020
  12. Feb 08, 2020
  13. Feb 07, 2020
    • Alex Kanitz's avatar
      fix various small issues · 17818f4a
      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
      17818f4a
  14. Jan 24, 2020
  15. Dec 20, 2019
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