ViroConstrictor v1.0.1

Bug Fixes

• correctly exit amplicon_coverage calc when only one side of an amplicon could be found combined with low coverage samples (aa77006)
• ensure the split reference sequences are always in uppercase (fcf034c)

ViroConstrictor v1.0.0

⚠ BREAKING CHANGES

• Use a single coverage level during analysis, defaults to 30 (6d6fc01)
• add support for per-sample analysis settings with an input samplesheet in Excel, TSV or CSV format (a0b726)
• Add support for BED files in amplicon_covs (ece3dfa)
• Use BED files as output of AmpliGone (79fd23)
• Update to python version 3.10 in base environments. (minimal required version = 3.8) (184328)
• Use a single coverage level for TrueConsense (e5701b9a)

Features

• flexible snakemake rule_all based on samplesheet inputs (93ad0c)
• use the snakemake Paramspace for wildcard generation (94d1738)
• Add remove_adapters_p1 to all (64c9069)
• Add remove_adapters_p2 and qc_filter to all (a89560)
• Add prepare_primers (6dc7c9)
• Add prepare_gff rule (a0bc0fb)
• Re-add ampligone (89cc2a0)
• Re-add qc_post to multiqc (45c0d12)
• Re-add TrueConsense (44f36c1)
• Re-add concat_seq (ab229de)
• Re-add tsv output (5bf10aa)
• Re-add breadth of coverage to snakefile (003b2f)
• Re-add amplicon_cov (6f6088)
• Correctly handle missing inputs in samplesheet (aa6995)
• re-add illumina support in new workflow structure (8eb400)
• add fastP stats to multiqc report (19627f)

Bug Fixes

• Add option to not give primers on cli (e4c054c)
• Check combination of samplesheet and cli args (e4c054c)
• Fix broken snakefile (a704c5e)
• Add .bed as filetype for primers (f16556)
• Make prodigal and prepare_gff unique (761337)
• Fix aggregation outputs to rule all (2269340)
• Fix restructuring of results folder (76fda46)
• group concatenated files in correct results subfolders (f3f1d9e)
• Make sure all post_qc is added in multiqc (b51f0ce)
• Remove excess bracket in various log&bench rules (4a5e96c)
• add logs for calculate_amplicon_cov rule (fbd2c1c)
• always use absolute path for input reference, primer and features files (fa68a7a)
• always provide absolute path for input fastq files (0303244)
• Raise error if fasta contains invalid char (5209a7b)
• Bump minimum snakemake version (a31b503)
• change multiqc memory requirements to 'high' (05b9db3)
• filter input primer bedfile to only output matching refID bedfile (c2b9c0c)

Code Refactoring

• move version to init file (e4c054c)
• Remove empty.primers (bfe0044)
• use the snakemake Paramspace wildcards in the multiQC aggregation (1204b09)
• add the "extract_refs.py" script to repo (5a7ea4)
• move multiqc input function to top of snakefile (1134bb)
• use new prepare_primers rule in new structure (4d06939)
• use new prepare_gffs rule with the new structure (537d09)
• add basic gff filter script (09ada9)
• Refactor with bottum up approach (682cafa)
• Rename Sample to sample (a6c0e48)
• Change to wc_pattern (214e21)
• Switch wc_pattern to wc_folder (40d4d2e)
• Remove threads: 1 as it is default (5cd6ca6)
• Make wildcard notation consistent (8fe4f7e)
• Re-ordering of code (b3d891)
• Remove mincov variable in snakefile (5bb47a9)
• change used fonts in the generated report to accomodate fpdf2 (5bb91d1)
• merge if statement blocks to singular condition (7b2882f)
• simplify boolean returns (615d2cf)
• use new expression for conditional in samplesheet generator (8ca585a)

Dependencies

• update AmpliGone to version 1.0.1 (e4c054c)
• update TrueConsense version to v0.4.0 ([e4c054c](https://www.github.com/RIVM-bioinformatics/V...

ViroConstrictor v0.4.2

Bug Fixes

• limit the self-updater to only update minor and patch versions (f864f55)

ViroConstrictor v0.4.1

Bug Fixes

• correct the memory assignment and threads for RemovePrimers job when no primers are given (a9ebe02)

ViroConstrictor v0.4.0

Features

• add an adjustable mismatch rate for the primer search (7fc4265)
• dynamically set usable cpus/threads in local execution mode (1ec85bb)
• Write a short report with the used/configured settings of the analysis (0c46366)

Bug Fixes

• add missing --skip-updates flag (f360161)
• corrected update function parameters (7f37d90)
• finish an analysis when empty input fastq files are given (d178587)
• properly exit with right exit codes and print closing message (f1bbe13)

Performance Improvements

• tweak read qc filtering settings (b3aab5a)
• use adjusted mm2 mapping settings in nanopore-mode (c027daa)

Dependencies

• add FPDF version 1.7.2 to dependency lists (cfcd9ee)
• add lenient version requirements to mamba (07ebfcc)
• add urllib3 v1.26 to dependency list for the auto-updater (cfcd9ee)
• change biopython version in python setupfile (07ebfcc)
• change pysam to lenient versioning (cfcd9ee)
• inlcude conda (lenient) version 4.11.x in main env for compatibility (cfcd9ee)
• pin pysamstats version to 1.1.2 (cfcd9ee)
• pin tqdm (lenient) version to 4.62.x (cfcd9ee)
• pin TrueConsense to version 0.3.0 (cfcd9ee)
• remove pysamstats from 'clean' environment (cfcd9ee)
• update AmpliGone 0.4.0 --> 0.4.1 (ea06728)
• update AmpliGone 0.4.1 --> 0.4.3 (af62d22)
• update AmpliGone version 0.2.3 --> 0.4.0 (cfcd9ee)
• update bcftools 1.12 --> 1.14 (cfcd9ee)
• update bedtools 2.29.2 --> 2.30.0 (cfcd9ee)
• update biopython 1.78 --> 1.79 (cfcd9ee)
• update fastp 0.20.1 --> 0.23.2 (cfcd9ee)
• update fastqc 0.11.8 --> 0.11.9 (cfcd9ee)
• update minimap2 & mappy 2.17 --> 2.24 (cfcd9ee)
• update multiqc 1.9 --> 1.11 (cfcd9ee)
• update pandas 1.2.3 --> 1.3.5 (cfcd9ee)
• update parmap 1.5.2 --> 1.5.3 (cfcd9ee)
• update PyYaml 5.4.1 --> 6.0 (cfcd9ee)
• update samtools 1.11 --> 1.14 (cfcd9ee)
• update seqkit 0.14.0 --> 2.1.0 (cfcd9ee)
• update snakemake 6.4.1 --> 6.13.1 (cfcd9ee)

Documentation

• add importance of primer name and number to docs (7107398)
• include primer mismatch rate flag to documentation (531f526)
• update installation instructions (5944d22)

ViroConstrictor v0.3.0

Features

• allow ViroConstrictor to update itself to latest release (11ad616)
• flexible memory requirements per workflow job (7c189cd)

Bug Fixes

• change consensus calling to a 'mid' cpu-task (3094b78)

ViroConstrictor v0.2.3

Documentation

• add explanatory comments to docs config (f3e05ec)

ViroConstrictor v0.2.2

Bug Fixes

• change amplicon covs script to complete with empty input #5 (6900638)
• complete workflow with primers set to NONE (47becf8)
• use 'map-ont' mm2 preset in nanopore workflow (f89d5cf)

First release: ViroConstrictor 0.2.1

Initial versioned release of ViroConstrictor with version 0.2.1

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences from your data based on a given reference genome.

ViroConstrictor performs high speed data quality control, data cleanup, and high accuracy removal of primer-sequences from NGS reads. As well as alignment of reads and generation of a consensus sequence using the TrueConsense consensus-caller which accounts for common sequencing errors and alignment artefacts.