Changelog

0.6.8 (2024-07-03)

Dependencies

• Update conda environment files to remove the 'intel' channel (4572252)

Documentation

• update documentation page accordingly (4572252)

0.6.7 (2024-04-04)

Bug Fixes

• properly handle empty index files (0ee4d74)

Dependencies

• explicitly state the nodefaults channel in all environments (749ad4a)
• remove anaconda and defaults channels from conda recipes (e201894)
• solve minor installation hassles for the main environment (749ad4a)

0.6.6 (2023-03-01)

Dependencies

• Update AmpliGone to v1.2.1 (67706ff)

0.6.5 (2023-01-17)

Code Refactoring

• re-balance threads to improve parallelization in local execution mode (use at most n threads for certain steps) (a8bccad)

0.6.4 (2022-10-10)

Dependencies

• set tabulate version to 0.8.10 in Typing environment as workaround (a391864)

0.6.3 (2022-10-10)

Dependencies

• pin python-tabulate to v0.8.10 as a workaround for snakemake (3766878)

0.6.2 (2022-08-23)

Bug Fixes

• change the directory with nextclade dataset from temp to non-temp in order to circumvent a WorkflowError (ae3da11)

0.6.1 (2022-08-15)

Bug Fixes

• write AmpliGone output to logfile instead of stdout (ff16fe4)

Dependencies

• simplify the QC_and_cleanup environment (8a8059e)
• update Nextclade to newer (lenient) version 2.4.x (d5b90e2)
• Update required snakemake version to 7.x (pinned to 7.12.1) (b171fc4)
• upgrade AmpliGone to version 1.1.0 (ec005aa)
• use the bioconda channel to install AmpliGone instead of pip (8a8059e)

0.6.0 (2022-04-26)

Features

• Update TrueConsense to 0.5.0 (972c08a)

Bug Fixes

• Update Ampligone to 1.0.1 (cce0e31)

0.5.4 (2022-04-08)

Dependencies

• pin pangolin version number to 4.0.2 without auto-updating (27e30d3)

0.5.3 (2022-04-05)

Bug Fixes

• allow pangolin v4 empty output when there's low coverage in the typing sequence (3237202)

0.5.2 (2022-04-04)

Dependencies

• add python3.7 to Alignment env to stabilize environment during installation (6f1387d)
• change Typing rules and packages for compatibility with pangolin v4.* (81a61d5)

0.5.1 (2022-02-04)

Bug Fixes

• finish an analysis when empty input fastq files are given (7a30b18)

Dependencies

• update AmpliGone 0.4.0 --> 0.4.1 (cf64dc4)
• update AmpliGone 0.4.1 --> 0.4.3 (28baf2a)

0.5.0 (2022-01-27)

Features

• Write a short report with used/configured settings of the analysis (ffe3141)

Bug Fixes

• properly exit with right exit codes (4ec6307)
• sucessfully finish an analysis when no primers are given (4916731)

Performance Improvements

• tweak read qc filtering settings (27916d4)

Dependencies

• add FPDF version 1.7.2 to dependency list(s) (1a192ec)
• add urllib3 to dependency list for the auto-updater (f3b9b53)
• include conda (lenient) version 4.11.x in main environment to circumvent python3.10 bug (a7821f4)
• remove pysamstats from 'clean' environment (485c94e)
• update (pangolin) snakemake 6.4.1 --> 6.8.0 (1ffc79d)
• update AmpliGone version v0.3.3 --> v0.4.0 (999b757)
• update bcftools 1.12 --> 1.14 (9108076)
• update bedtools 2.29.2 --> 2.30.0 (9108076)
• update biopython 1.78 --> 1.79 (9108076)
• update biopython to version 1.79 in main environment (43251f0)
• update FastP to version 0.23.2 (b134b64)
• update fastqc 0.11.8 --> 0.11.9 (485c94e)
• update minimap2 & mappy 2.17 --> 2.24 (cb99be4)
• update multiqc 1.9 --> 1.11 (485c94e)
• update nextclade 1.6.0 --> 1.9 + change to lenient versioning (1ffc79d)
• update nextclade lenient version v1.9.x --> v1.10.x (2e1cf9e)
• update pandas 1.2.3 --> 1.3.5 (485c94e)
• update pangolin 3.0 --> 3.1 + change to lenient versioning (1ffc79d)
• update parmap 1.5.2 --> 1.5.3 (485c94e)
• update PyYaml 5.4.1 --> 6.0 and fix compatibility (e9a1ef9)
• update samtools 1.10 --> 1.14 (cb99be4)
• update seqkit 0.14.0 --> 2.1.0 (cb99be4)
• update snakemake to version 6.13.1 in main environment (43251f0)
• update tqdm 4.59 --> 4.62 (485c94e)

Documentation

• add extra primer keywords (422f192)
• fix typo in docs and update download instructions (9f239e3)
• update readme with correct primer-keywords (17878f8)
• update snakemake version label (f1a474d)

0.4.2 (2021-12-08)

Dependencies

• remove manual installation of pango-designations repo (5527d53)
• update AmpliGone to version 0.3.3 (b97a32e)
• update nextclade typingtool to version 1.6.0 (303d4d9)

0.4.1 (2021-11-26)

Dependencies

• update AmpliGone to version 0.3.2 (d47f62b)

0.4.0 (2021-11-25)

Features

• allow SARS2seq to update itself to latest release (41b711b)
• override consensus-index with overlap coordinates index (b81fd1c)

Bug Fixes

• Remove --end-bonus and -k28, update -A4 (e7f8bf7)
• update sars-cov-2 genomic features GFF to include missing ORF (4399cf4)

Performance Improvements

• Update minimap2 settings for nanopore data (75bb475)

Documentation

• add (auto-)updating behaviour and "skip-updates" flag to documentation (43c3655)

Dependencies

• pin TrueConsense to version 0.3.0 (b6dfd46)
• update AmpliGone to version 0.3.0 (f028403)
• update AmpliGone to version 0.3.1 (29f1516)

Styles

• remove trailing space (9933ab4)

0.3.0 (2021-11-09)

Features

• flexible memory requirements per workflow job (dd1c89e)

Bug Fixes

• use 'map-ont' mm2 preset in nanopore workflow (87e056c)