1.2.0 – Norwegian Ridgeback

[1.2.0] – Norwegian Ridgeback - [2023-12-19]

Enhancements & fixes

• Restored recording read-groups (@RG) in the BAM/CRAM files.
• Updated the CI procedure to use "sanger-tol" rather than "nf-core" names.
• crumble now used to compress the
  PacBio HiFi alignments.
• Execution statistics now under pipeline_info/readmapping/ (to be consistent
  with the other sanger-tol pipelines).
• All resource requirements (memory, time, CPUs) now fit the actual usage. This
  is achieved by automatically adjusting to the size of the input whenever
  possible.
• Added the --use_work_dir_as_temp parameter to make SAMTOOLS_COLLATE use its
  work directory for temporary files instead of $TMPDIR. It can be used to avoid
  leaving unwanted temporary files on a HPC.

Parameters

Old parameter	New parameter
	--use_work_dir_as_temp

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
blast	2.12.0	2.13.0
crumble		0.9.1
samtools	1.14 and 1.16.1	1.14 and 1.17
multiqc	1.13	1.14

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.