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  • BIOPZ-Katsantoni Maria's avatar
    6cf28511
    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
    History
    Major refactoring
    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