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  1. May 07, 2021
  2. Feb 26, 2021
  3. Feb 11, 2021
  4. Jun 23, 2020
  5. Apr 27, 2020
    • BIOPZ-Katsantoni Maria's avatar
      Major refactoring · 6cf28511
      BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed
      * 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
      6cf28511
    • CJHerrmann's avatar
      Add rules for bigWig creation · 907082c3
      CJHerrmann authored and Alex Kanitz's avatar Alex Kanitz committed
      907082c3
  6. Mar 25, 2020
  7. Mar 20, 2020
    • Dominik Burri's avatar
      extend ALFA functionality · f5e2f6ac
      Dominik Burri authored and Alex Kanitz's avatar Alex Kanitz committed
      - generate nucleotide distribution for unique reads only
      - new rule to generate PNG image for MultiQC
      f5e2f6ac
    • 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
  8. Mar 19, 2020
  9. Mar 17, 2020
  10. Mar 12, 2020
  11. Mar 06, 2020
  12. Feb 21, 2020
  13. Feb 15, 2020
    • BIOPZ-Katsantoni Maria's avatar
      get Snakemake input from LabKey API · eea0206f
      BIOPZ-Katsantoni Maria authored and Alex Kanitz's avatar Alex Kanitz committed
      - 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
      eea0206f
  14. Feb 09, 2020
    • Alex Kanitz's avatar
      replace test files with small synthetic ones · 48e012a0
      Alex Kanitz authored
      - replaces existing larger libraries and annotations in test cases `test_create_dag_chart` and `test_integration_workflow`
      - adds the following new test files:
        - `chr1-10000-20000.fa`: artificial chromosome of length 10'000 (based on human chromosome 1)
        - `chr1-10000-20000.gtf`: matching gene annotation file with two gene and three multi-exon transcripts entries
        - `chr1-10000-20000.transcripts.fa`: sequences of the transcripts listed in the gene annotation file
        - `synthetic.mate_?.fastq.gz`: 10 read pairs randomly sampled from the genic regions of the artificial chromosome
        - `synthetic.*.bed`: BED files with expected alignments for each read; names of overlapping genes are specified in a 7th column
      - updates file paths in the relevant sample tables
      - extends and updates checksum checking of result files in CI/CD pipeline
      48e012a0
  15. Feb 08, 2020
  16. 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
  17. Feb 04, 2020
    • Alex Kanitz's avatar
      clean up tests · 6a231363
      Alex Kanitz authored
      - set up integration test for Snakefile in dedicated folder; current test case was left untouched for the time being, despite requiring large input files
      - set up DAG chart creation test in dedicated folder; script creates an SVG representation of the workflow DAG at `images/workflow_dag.svg`
      - both tests have been added to the GitLab CI/CD configuration; the latter test ensures that always the latest version of the
      - all tests are now located inside subdirectories of `tests/`; test scripts and configuration files for test runs etc. have been moved to the appropriate test directories
      - for the time being, required input files for each test are placed within the individual test directories; a layout for common test files should be introduced later and paths and bind paths in tests adapted
      - make script `scripts/labkey_api.py` executable
      6a231363
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