sanger-tol/readmapping v2.0.0 - Hungarian Horntail

[v2.0.0] - Hungarian Horntail - [2026-04-27]

Enhancements & fixes

• Add Blobtk depth to calculate read coverage
• Add FastQC for quality control of reads
• Add Lima to trim ULI adapter and demultiplex ULI reads. In case the reads are already trimmed/demultiplexed, this process can be skipped by setting --pacbio_uli_adapter to false.
• Add pbmarkdup to remove ULI duplicates
• Add hifi-trimmer instead of HifiAdapterFilt approach to filter PacBio reads. Disable by setting --pacbio_adapter_fasta and --pacbio_adapter_yaml to false
• Align data in chunks with sanger-tol/cram_map_long_read and sanger-tol/cram_map_illumina_hic
• Add MultiQC to aggregate quality control statistics
• Migrate local modules to nf-core and sanger-tol central modules repository
• Replace sample column in samplesheet with specimen & run; and update output structures accordingly (see outputs.md)
• Upgrade Samtools version to allow CRAM, archive, level 8
• Remove read names in output short-read CRAM files to reduce file size
• Compress samtools stats files to reduce storage usage
• Switched to not merging alignments by specimen by default. Merged alignment can be re-enabled with the new --merge_output.
• Perform CRAM file reheadering after converting BAM to CRAM (previously done before conversion) to ensure provided headers are retained

Parameters

| Old parameter | New parameter | | ----------------- | ------------------------------ | | --vector_db | | | --bwamem2_index | | | | --pacbio_adapter_fasta | | | --pacbio_adapter_yaml | | | --pacbio_uli_adapter | | | --short_aligner | | | --long_reads_map_chunk_size | | | --short_reads_map_chunk_size | | | --merge_output | | | --window_size |

NB: Parameter has been updated if both old and new parameter information is present. </br> NB: Parameter has been added if just the new parameter information is present. </br> 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 | | -------------- | ----------- | ----------- | | blastn | 2.15 | 2.17 | | bwa-mem2 | 2.2.1 | 2.3 | | blobtk depth | | 0.7.1 | | fastqc | | 0.12.1 | | gawk | | 5.3.0 | | hifi-trimmer | | 2.2.0 | | lima | | 2.12.0 | | minimap2 | 2.28 | 2.30 | | multiqc | | 1.33 | | pbmarkdup | | 1.2.0 | | pigz | | 2.8 | | samtools | 1.21 | 1.23.1 |

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