1.3.1 Antipodean Opaleye (patch 1)

[1.3.1] - Antipodean Opaleye (patch 1) - [2024-09-24]

Enhancements & fixes

• Fixed bug in handling CRAM HiC inputs introduced in 1.1.0
• Fixed bug in handling PacBio FASTQ inputs introduced in 1.3.0

Dependency	Old version	New version
bbtools		39.01
seqtk	1.4

1.3.0 - Antipodean Opaleye

[1.3.0] - Antipodean Opaleye - [2024-08-23]

Enhancements & fixes

• Combined steps to improve the efficiency of the pipeline, especially on large genomes
• "crumble" is now run on every data type, not just PacBio
• Added options for output format and to turn on/off crumble compression (#107)
• Added fastq as possible input type for PacBio (#106) and Illumina/HiC (#96)
• Disabled running bwa index when no short-read data provided (#100)
• Added support for optional custom SAM header (#95)
• Switch to nf-validation (#99) and further updates for nf-core v2.14 compliance (#98)

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
blastn	2.13	2.15
minimap2	2.24	2.28
samtools	1.14 and 1.17	1.20
seqkit		2.8.1
seqtk		1.4

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.

Parameters

Old parameter	New parameter
	'--header'
	'--outfmt'
	'--compression

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.

1.2.2 – Norwegian Ridgeback (patch 2)

[1.2.2] - Norwegian Ridgeback (patch 2) -[2024-05-23]

Enhancements & fixes

• Fixed the bug in the filtering of multiple PacBio files

1.2.1 – Norwegian Ridgeback (patch 1)

[1.2.1] - [2024-02-29]

Enhancements & fixes

• Increased the memory requests for reruns of BWAMEM2_MEM and SAMTOOLS_SORMADUP.

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.

v1.1.0 – Hebridean Black

[1.1.0] – Hebridean Black - [2023-03-16]

Enhancements & fixes

• Bump minimum Nextflow version from 22.04.0 -> 22.10.1
• Updated pipeline template to nf-core/tools 2.7.1
• Added nf-core modules to replace most local modules
• Added improved resource settings
• Added support for unit and full tests on Sanger HPC via Nextflow Tower
• Added all unit test data on a S3 bucket
• Added statistics subworkflow functionality to the alignment subworkflows
• Removed support for iGenomes
• Removed samtools faidx and minimap index module, it now happens on the fly

Parameters

Old parameter	New parameter
--enable_conda
--minimap2_index
--samtools_index

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
minimap2	2.21	2.24
samtools	1.15 and 1.15.1	1.14 and 1.16.1
multiqc	1.11 and 1.12	1.13
bam2fastx	1.3.1
pbbam	2.1.0

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.

v1.0.0 – Ukrainian Ironbelly

Initial release of sanger-tol/readmapping pipeline, created with the nf-core template.

⚠️ Major Enhancements

• HiC and Illumina read alignment to genome
• PacBio CLR and CCS read alignment to genome after filtering
• Nanopore read alignment to genome
• Mark duplicates for HiC and Illumina alignments
• Convert to CRAM and calculate statistics for all alignments

Dependencies

• nextflow 22.04.0 or later
• singularity or docker