CHANGELOG.md

nf-core/isoseq: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.1.1 - White Hawk [26/09/2022]

Update the pipeline to nf-core 2.5.1, update modules, and fix documentation.

Added

Fixed

• Documentation: Correct aligner option documentation

Dependencies

• Update samplesheet_check module
• Update dumpsoftwareversion module
• Update MultiQC module

Deprecated

v1.1.0 - Black Crow [12/07/2022]

Improves computation time. Split uLTRA pipeline into two processes, uLTRA index and uLTRA align. GTF index is computed once and not chunk times. uLTRA align sort and convert sam output into bam files. Aligned reads are already sorted by minimap2 module. Therefore, samtools sort module is not needed anymore and has been removed. The bioperl module objective was to deal with spurious alignments produced by uLTRA if a malformed GTF is used. Removing it will stop the pipeline in case of malformed GTF. Module resource requirements have been revised for four modules (gstama/merge, isoseq3/refine, lima, ultra/align) to reduce requested resources. AWS runs with shows better run time and CPU/RAM usage (Results).

Added

• Add uLTRA index and uLTRA align to replace uLTRA pipeline PR 1830
• Module resources adjustments: gstama/merge, isoseq3/refine, lima, ultra/align PR1858, gunzip, MultiQC

Fixed

Dependencies

Deprecated

• Remove uLTRA pipeline
• Remove samtools sort module
• Remove bioperl module

v1.0.0 - Silver Swan [28/06/2022]

Initial release of nf-core/isoseq, created with the nf-core template.

Added

Fixed

Dependencies

Deprecated