v1.3.0

Added

• Workflow will generate VCF index file if it doesn't exist.

Fixed

• Set format of --bam and --fastq in schema to path, to enable directories to be selected as input in the EPI2ME application.

Removed

• Empty alignment stats plots which are not relevant to this workflow.

[v1.2.2]

Fixed

• Capitalised modified base tags additionally removed from monomers if no modified bases for a monomer.

v1.2.1

Fixed

• bamindex fetch error when running more than one sample and --chunk_size is greater than 0.

v1.2.0

Fixed

• --bed parameter will now output BED file using the paired_end BAM file.
• Reduce memory usage of BED file creation and sorting.
• Increased memory allocation for prepare_hic and merge_mcool processes.
• If sample sheet provided and cutter column not present the workflow will instead use --cutter parameter.

Changed

• Bump pore-c-py to v2.1.4 to prevent issues with modified base tags and strip minimap2 tags from inputs.

Added

• Reduce peak memory usage of minimap2 by adding --cap-kalloc 100m --cap-sw-mem 50m to the minimap2 command in the digest_align_annotate process.

v1.1.0

Added

• --bed parameter which if set to true will output a BED file that is compatible with downstream tools including the scaffolder Yahs.
• --pairtools_chunksize parameter which exposes pairtools dedup chunksize parameter, in case peak memory usage of hi_c process needs to be reduced.
• digest_align_annotate process uses dedicated pore_c_py container.
• --max_monomers parameter, which is set to 250 by default, will filter out any reads that have more than this number of monomers. These reads will not be included in the analysis.
• Output a filtered_out/{alias}.bam with any reads that are filtered out due to the max_monomers parameter.

v1.0.0

Changed

• New documentation.

v0.2.0

Fixed

• Pairtools merge step single quote the input directory so it will not error with Argument list too long.
• Chromunity parquet files now contain the correct column names.

Changed

• --ubam parameter has been renamed --bam
• All other ubam related parameters have been renamed with bam for consistency
• The --bam_map_threads, --digest_annotate_threads and bam_bam2fq_threads threading parameters are now automatically extracted from the --threads specifying the maximum number of threads to use for a process.

Removed

• Default local executor CPU and RAM limits.

v0.1.1

Changed

• If --hi_c parameter set to true the pairs file will be created.

v0.1.0

Changed

• GitHub issue templates
• Nextflow minimum version 23.04.2.
• --sample_id parameter has been changed to --sample for consistency.
• --summary_json optional parameter with default set to true, to include an annotation summary json in outputs.
• Remove --params_sheet parameter and add all per sample parameters to sample_sheet.

Added

• --hi_c optional parameter with default set to false, to include a .hic output file which is compatible with Juice box.

v0.0.8

• Improve schema parameter explanations and output file descriptions in the README.
• Add a default --chunk_size parameter value of 25000.
• Update fastcat which removes need to index ubam.
• Enum choices are enumerated in the --help output.
• Enum choices are enumerated as part of the error message when a user has selected an invalid choice.
• Bumped minimum required Nextflow version to 22.10.8.

Fixed

• Replaced --threads option in fastqingress with hardcoded values to remove warning about undefined param.threads

v0.0.7

Fixed

• Testing for the cooler tool.