Ribodetector and RustQC Additions#47
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- Implemented ribodetector rules and associated conda environment - Implemented RustQC and added singularity requirement in job script to run it. - Updated multiqc config to support branding to CQB and new QC report - IMplemented basic QC report (what we previously had) and detailed QC report
Removed script parameter from ribodetector rule.
- Rename `env_configs` with `rna` prefix - Create Dockerfiles based on `singularity/defs` - Host containers on ghcr
- Update `env_config` yaml name in `conda` directives - Add `container` directives to point to ghcr location
- Add toggleable params (ribodetector, rustQC, Rsem) as separate rules - Add `build_refs` and `check_refs` as separate rules - Add `hisat.smk` and `star.smk` to clean up main `Snakefile`
- Also add `job.script.conda.sh` for conda support
In shell call, the first argument to `ribo_stats.sh` needs to be relative to the `additional_rules/ribodetector` so `../../` is needed.
- `rg ID` becomes `--rg-id` - Fix path bug in `ribodetector.smk`
- Script crashes when `sns.clustermap` has recursion error. Wrap the clustering in a `try/except` block so script doesn't exit when non-zero clustering fails. Instead, it prints a warning, let's the script exit safely
…rity Restructuring and Singularity Support
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Ribodetector
snakefilescripts/ribo_stats.shto generate ribs statistics compatible with MultiQCRustQC
job.script.shif run_rustqc is trueGeneral linting
config.yamland allprebuilt_configsfor ribodetector and rustQC