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  1. Aug 20, 2021
  2. Jul 14, 2021
  3. Apr 15, 2021
  4. Mar 25, 2021
    • BIOPZ-Katsantoni Maria's avatar
      Remove extra parameters, that had or should have the default values · 5396adf5
      BIOPZ-Katsantoni Maria authored and BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos committed
      and are therefore not required in the rules.
      - Snakefile
       star_rpm: --outWigNorm (default RPM was used)
       star_rpm: --outWigStrand (default Stranded was used)
       rename_star_rpm_for_alfa: orientation in params is redundant (Fixes #152)
      - single_end.snakefile.smk
       map_genome_star: outFilterMismatchNoverLmax
       map_genome_star: outFilterScoreMinOverLread
       map_genome_star: outFilterMatchNminOverLread
       quantification_salmon: --writeUnmappedNames
      - paired_end.snakefile.smk
        pe_map_genome_star: outFilterMismatchNoverLmax
        pe_map_genome_star: outFilterScoreMinOverLread
        pe_map_genome_star: outFilterMatchNminOverLread
        quantification_salmon: --writeUnmappedNames
      5396adf5
  5. Feb 11, 2021
  6. Oct 16, 2020
  7. Jun 23, 2020
  8. Jun 12, 2020
  9. Apr 28, 2020
    • Alex Kanitz's avatar
      Extend workflow description · 80453305
      Alex Kanitz authored
      - add linked ToC
      - add table of third party software
      - add rule graph
      - clean up sample table description
      - formalize structure for each rule description
      - cross-reference rules via inputs/outputs
      - clean list of references
      80453305
  10. Apr 27, 2020
  11. Mar 25, 2020
  12. Mar 20, 2020
    • BIOPZ-Katsantoni Maria's avatar
      update of documentation · 46689ffd
      BIOPZ-Katsantoni Maria authored
      46689ffd
    • 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
  13. Mar 19, 2020
  14. Mar 13, 2020
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