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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
expected_output.md5 17.84 KiB 
cbaebdb67aee4784b64aff7fec9fda42  results/kallisto_indexes/homo_sapiens/kallisto.idx
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51b5292e3a874119c0e1aa566e95d70c  results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
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dee7cdc194d5d0617552b7a3b5ad8dfb  results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
8e2e96e2d6b7f29940ad5de40662b7cb  results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
d0826904b8afa45352906ad9591f2bfb  results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
8d3291e6bcdbe9902fbd7c887494173f  results/star_indexes/homo_sapiens/75/STAR_index/chrStart.txt
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