refactor: optimize process labels, tune slurm executor settings, adju…#73
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…st default params refactor: update cpus, memory, and time in base.config process label definitions refactor: reassign process labels in module main.nf to better match actual resource needs refactor: tune SLURM executor settings in slurm.config (pollInterval, queueStatInterval, submitRateLimit, exitReadTimeout) refactor: adjust default params in nextflow.config refactor: add process-specific time limits in modules.config (e.g. MSCONVERT_MZML) fix: hardcoded 'merged' meta.id in pacbio_isocall.nf to use params.dataset_name (edited) fix: removes spaces from BED12 name field in novel_peptide.R
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…st default params
refactor: update cpus, memory, and time in base.config process label definitions
refactor: reassign process labels in module main.nf to better match actual resource needs
refactor: tune SLURM executor settings in slurm.config (pollInterval, queueStatInterval, submitRateLimit, exitReadTimeout)
refactor: adjust default params in nextflow.config
refactor: add process-specific time limits in modules.config (e.g. MSCONVERT_MZML)
fix: hardcoded 'merged' meta.id in pacbio_isocall.nf to use params.dataset_name (edited)
fix: removes spaces from BED12 name field in novel_peptide.R
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).