v0.12.5

Bug fix release to report the correct version. Previous version 0.12.4 was incorrectly reporting the version as 0.12.3

v0.12.4

Add vcf/fasta filter/mask options to clockwork variant_call_one_sample: --filter_min_dp, --filter_min_frs, --filter_min_gcp, --filter_max_dp, --fasta_allow_minos_filter_fail, --fasta_min_frs, --fasta_min_dp

v0.12.3

Bug fixes for ENA submissions, for where there is more than one run for a sample

v0.12.2

• Gracefully handle edge cases with variant_call_one_sample: cortex failing, empty reads files, missing reads files (#115)
• Fixed bug in remove_contam when using more than one pair of input files (#116)
• Fixed bug when making GVCF file, code was assuming DP was int instead of float (4f4df7b)
• Add tag DP_ACGT to GVCF file (#118)

v0.12.1

Add option --no_trim to clockwork variant_call_one_sample to not trim reads

v0.12.0

• Update human genome to CHM13
• Variant call pipeline writes GVCF file, and fasta for MSAs that ignores indels
• fix for failing container builds by pinning nextflow to 22.10.0, which supports DSL1

v0.11.3

• update minos 0.12.5
• fix urls in decontamination download

v0.11.2

• update mykrobe 0.12.1
• update minos 0.12.4
• bug fix with variant_call_one_sample and sample names of 6 characters (issue #98)

v0.11.1

Bug fix: v0.11.0 was missing the script download_tb_reference_files.pl

v0.11.0

• Use minimap2 instead of BWA. This code will work on existing reference directories made by clockwork reference_prepare. It will use the FASTA file in the directory. But if you rerun clockwork reference_prepare then it will make a minimap2 index file, saving indexing on the fly. This probably makes little difference for variant calling, but could make a difference when running decontamination because that reference is huge.
• Auto build singularity and docker containers
• Updates to the decontamination reference download scripts because accessions change etc.