CHARLIE: Circrnas in Host And viRuses anaLysis pIpEline

CHARLIE 0.13.0

• Migrate runtime activation to a mamba-safe flow to avoid shared-environment activation failures. (#149, @kopardev)
• Host-only circRNA discovery is now supported. Additives (e.g. ERCC) and viruses are now fully optional — omitting them runs the pipeline in host-only mode, a long-standing user request. Make host/additives/viruses config placeholders envsubst-compatible and default additives to blank when omitted. (#149, @kopardev)
• Replace hard-coded CCBR base paths under /gpfs with /vf for current filesystem layout compatibility. (#149, @kopardev)
• Update Biowulf partition handling by removing deprecated ccr usage and forcing/defaulting to norm. (#149, @kopardev)
• Align onsuccess/onerror completion hooks with CARLISLE behavior while preserving CHARLIE's shared hook implementation, including stricter shell setup and completion-log checks. (#153, @kopardev)
• Auto-detect $SIFCACHE (set by module load ccbrpipeliner) and use it as the singularity cache and --singularity-prefix so Snakemake finds pre-downloaded SIF files without pulling from Docker Hub. (#154, @kopardev)
• Print a configuration summary block (workdir, snakefile, config, singularity cache, binds, platform) to the terminal before each pipeline run. (#154, @kopardev)
• Fix set_singularity_binds not being called in unlock(), dryrun(), and touch(), which left SINGULARITY_BINDS empty. (#154, @kopardev)
• Smarter singularity bind path detection: walk up parents of WORKDIR and PIPELINE_HOME to find /data/<name> symlinks and include both the symlink and real path; filter Python-derived paths that are ancestors (too broad) or descendants (too specific) of the bash-derived explicit paths. (#154, @kopardev)