From 97fdaac7967e8c2af3a2cc39f5234308e150b661 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 21 Mar 2022 10:59:04 +0100 Subject: [PATCH] chore(master): release 0.14.0 (#446) * chore(master): release 0.14.0 * Changed containerized tag to 0.14.0 Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] --- CHANGELOG.md | 47 ++++++++++++++++++++++++++++++++++++++++++++++ version.txt | 2 +- workflow/Snakefile | 2 +- 3 files changed, 49 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c65a9fc6d..ebd5a74d8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,52 @@ # Changelog +## [0.14.0](https://github.com/IKIM-Essen/uncovar/compare/v0.13.2...v0.14.0) (2022-03-21) + + +### Features + +* add variant call details based on protein annotation ([#487](https://github.com/IKIM-Essen/uncovar/issues/487)) ([016bcfb](https://github.com/IKIM-Essen/uncovar/commit/016bcfb3721ed31b208b29a9bdab7957be32439d)) +* call known lineage variants ([#392](https://github.com/IKIM-Essen/uncovar/issues/392)) ([9ad720c](https://github.com/IKIM-Essen/uncovar/commit/9ad720c32f1b246b5ef8a20871063a05dfd682b8)) +* **deps:** bump github/super-linter from 4.8.6 to 4.8.7 ([#459](https://github.com/IKIM-Essen/uncovar/issues/459)) ([c18f241](https://github.com/IKIM-Essen/uncovar/commit/c18f2412f576b26050e3296bdcc509cd5facf462)) +* **deps:** update pangolin to 3.1.19 ([#461](https://github.com/IKIM-Essen/uncovar/issues/461)) ([3971687](https://github.com/IKIM-Essen/uncovar/commit/3971687db229577fa862b40f900701f18270011d)) +* **deps:** update pangolin to 3.1.19 ([#461](https://github.com/IKIM-Essen/uncovar/issues/461)) ([d5f42ca](https://github.com/IKIM-Essen/uncovar/commit/d5f42ca229c038adaf0ccb1ce772aaa4e229b1fe)) +* **deps:** update pangolin to 3.1.20 ([#467](https://github.com/IKIM-Essen/uncovar/issues/467)) ([78cb7f4](https://github.com/IKIM-Essen/uncovar/commit/78cb7f4452fe703194aed2fb393649572b60519c)) +* make incoming and archive structure data-handling optional ([#443](https://github.com/IKIM-Essen/uncovar/issues/443)) ([559e9c1](https://github.com/IKIM-Essen/uncovar/commit/559e9c1c1af503398a1669fd0e4f04e7d4b4a7ac)) +* make sending lab column in rki report csv adjustable via config file ([#492](https://github.com/IKIM-Essen/uncovar/issues/492)) ([311e857](https://github.com/IKIM-Essen/uncovar/commit/311e8578a7d9956ffb532314da60b01211a90b60)) +* rule and script bed_to_bedpe ([#447](https://github.com/IKIM-Essen/uncovar/issues/447)) ([3022eab](https://github.com/IKIM-Essen/uncovar/commit/3022eab0854992fb40894c7b1dd0feca8400b2fc)) + + +### Bug Fixes + +* add missing fasta index to vcf report ([#480](https://github.com/IKIM-Essen/uncovar/issues/480)) ([1697fb5](https://github.com/IKIM-Essen/uncovar/commit/1697fb50b2e4b3d249c4a83e83ecab2876118a91)) +* add missing voc variant report to environmental report ([#479](https://github.com/IKIM-Essen/uncovar/issues/479)) ([16baef1](https://github.com/IKIM-Essen/uncovar/commit/16baef1c440dbf6e059b81d2c3f7f100c53ee692)) +* bump rust-bio-tools to 0.38 ([#449](https://github.com/IKIM-Essen/uncovar/issues/449)) ([e85fa15](https://github.com/IKIM-Essen/uncovar/commit/e85fa15f0489185b9fc7a851005da1078c06c3fb)) +* canu and porechop logging ([5db0935](https://github.com/IKIM-Essen/uncovar/commit/5db09352abdcb2af41ae5b72250b26c547951877)) +* canu and porechop logs ([#473](https://github.com/IKIM-Essen/uncovar/issues/473)) ([497bfcd](https://github.com/IKIM-Essen/uncovar/commit/497bfcdd1bda588209295e7cc3e7d3acf20a2182)) +* **ci:** add missing missing echo to release please ([#476](https://github.com/IKIM-Essen/uncovar/issues/476)) ([6a0b899](https://github.com/IKIM-Essen/uncovar/commit/6a0b899454883d6c53c4234f2b356f20ac503249)) +* **ci:** change human reference from NC_000021.9 to BA000005.3 ([#488](https://github.com/IKIM-Essen/uncovar/issues/488)) ([14b4be0](https://github.com/IKIM-Essen/uncovar/commit/14b4be01ee1ff586b0e12d13b15c254d739e260b)) +* **ci:** change release please PR branch ([#481](https://github.com/IKIM-Essen/uncovar/issues/481)) ([603d3b5](https://github.com/IKIM-Essen/uncovar/commit/603d3b5edfbc7864e279950f8981c534397105d9)) +* **ci:** parse new json output from release please ([#474](https://github.com/IKIM-Essen/uncovar/issues/474)) ([eb598b7](https://github.com/IKIM-Essen/uncovar/commit/eb598b7f4feb51d8d5679dc2ef0aa823a7127a52)) +* **ci:** release please checkout branch ([#477](https://github.com/IKIM-Essen/uncovar/issues/477)) ([03a69bf](https://github.com/IKIM-Essen/uncovar/commit/03a69bfe23097222cf88f43f15d4b40b5f4fb3de)) +* correct filtering in plot-lineages-over-time ([#445](https://github.com/IKIM-Essen/uncovar/issues/445)) ([c71f72b](https://github.com/IKIM-Essen/uncovar/commit/c71f72bad90cc32923b7de6ffcc6de66367cf6ff)) +* **deps:** update multiqc wrapper ([#329](https://github.com/IKIM-Essen/uncovar/issues/329)) ([42fbcd8](https://github.com/IKIM-Essen/uncovar/commit/42fbcd8bc442d5c1e2142fc6c14406819c2b63bb)) +* fixed include flag KeyError ([#452](https://github.com/IKIM-Essen/uncovar/issues/452)) ([f47dad2](https://github.com/IKIM-Essen/uncovar/commit/f47dad20891a447e202aa2ff3f1712b77daaa593)) +* order of include flag sample ([#462](https://github.com/IKIM-Essen/uncovar/issues/462)) ([429e5d9](https://github.com/IKIM-Essen/uncovar/commit/429e5d9447b64dfbd20bcfaa924feb5fae7ddfb9)) +* pangolin plot color ([#483](https://github.com/IKIM-Essen/uncovar/issues/483)) ([9e368d5](https://github.com/IKIM-Essen/uncovar/commit/9e368d572abfb4816f8a3270b8deb22c198234ad)) +* reduce loading time of coverage plots ([#498](https://github.com/IKIM-Essen/uncovar/issues/498)) ([8a8f533](https://github.com/IKIM-Essen/uncovar/commit/8a8f53347aa90c66075c1418e9cdf34bbecc02bc)) +* remove removal of .indicators/replacement_notice.txt for int ([#457](https://github.com/IKIM-Essen/uncovar/issues/457)) ([c5b9f6c](https://github.com/IKIM-Essen/uncovar/commit/c5b9f6c02c6e65646d0bc748cef5962b56322b3e)) +* rename column header in report formatter ([#444](https://github.com/IKIM-Essen/uncovar/issues/444)) ([8ba21d9](https://github.com/IKIM-Essen/uncovar/commit/8ba21d90caa0e312e4619fc02e1a38f84039805b)) +* reset over table formatter ([#448](https://github.com/IKIM-Essen/uncovar/issues/448)) ([ee30a46](https://github.com/IKIM-Essen/uncovar/commit/ee30a46bc966413fbd1f8d616a3f1f97b356ff72)) +* untmp recalibrated bam ([#491](https://github.com/IKIM-Essen/uncovar/issues/491)) ([1118fd9](https://github.com/IKIM-Essen/uncovar/commit/1118fd91a815f002188ba9969ece6a159279953a)) +* VOC mutation table similarity calculation ([#484](https://github.com/IKIM-Essen/uncovar/issues/484)) ([82405ee](https://github.com/IKIM-Essen/uncovar/commit/82405ee8e1d0eddcf40315888ef3a32eda7b3954)) + + +### Performance Improvements + +* add ont temp flags ([#475](https://github.com/IKIM-Essen/uncovar/issues/475)) ([6447583](https://github.com/IKIM-Essen/uncovar/commit/6447583800b756c573bcf959d14d0d6f29eebd21)) +* ont downsampling normalisation ([#489](https://github.com/IKIM-Essen/uncovar/issues/489)) ([f502dd2](https://github.com/IKIM-Essen/uncovar/commit/f502dd287be37c76997f44054389124494e23ab7)) +* optimisations for ont - barcode+adapter-trimming, primer-trimming (porechop) and read correction (Canu) ([#454](https://github.com/IKIM-Essen/uncovar/issues/454)) ([e844fc4](https://github.com/IKIM-Essen/uncovar/commit/e844fc40923fcaa8c680079a05cd09173027fb00)) + ### [0.13.2](https://github.com/IKIM-Essen/uncovar/compare/v0.13.1...v0.13.2) (2022-01-06) diff --git a/version.txt b/version.txt index 9beb74d49..a803cc227 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -0.13.2 +0.14.0 diff --git a/workflow/Snakefile b/workflow/Snakefile index fda56fc2d..f820df3d1 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -21,7 +21,7 @@ report: "report/workflow.rst" container: "docker://condaforge/mambaforge" -containerized: "quay.io/uncovar/uncovar#0.12.0" +containerized: "quay.io/uncovar/uncovar#0.14.0" if config["strain-calling"]["use-gisaid"]: