From 7106afa390bdfdde8048d28ade9cff80b1187640 Mon Sep 17 00:00:00 2001 From: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Date: Mon, 6 Nov 2023 09:56:04 +0100 Subject: [PATCH 1/9] update pangolin to version 4.3 (#610) --- workflow/envs/pangolin.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml index 93a50ace..f6a26ad4 100644 --- a/workflow/envs/pangolin.yaml +++ b/workflow/envs/pangolin.yaml @@ -3,5 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - pangolin =4.1.3 - - tabulate <0.9 # TODO remove once pangolin 4.1.3 is available in bioconda + - pangolin =4.3 From 34701af485aa1ec199a418ec1487a97677f624ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 13 Nov 2023 13:03:17 +0100 Subject: [PATCH 2/9] perf: update to varlociraptor 8.4 (#596) * Update to latest varlociraptor * Update varlociraptor.yaml * Update config.yaml * trigger rerun --------- Co-authored-by: Alexander Thomas <77535027+alethomas@users.noreply.github.com> --- config/config.yaml | 6 +++--- workflow/envs/varlociraptor.yaml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index afea4a94..898b305a 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -72,12 +72,12 @@ assembly: # assemblers used for shotgun sequencing with on Illumina technology shotgun: "megahit-std" # assemblers used for amplicon sequencing with on Illumina technology - amplicon: "metaspades" + amplicon: "megahit-std" oxford nanopore: # assemblers used for shotgun sequencing with on Oxford Nanopore technology shotgun: "megahit-std" # assemblers used for amplicon sequencing with on Oxford Nanopore technology - amplicon: "spades" + amplicon: "megahit-std" # Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION or PromethION), iii) the basecaller variant, and iv) the basecaller version # with the format: {pore}_{device}_{caller variant}_{caller version} # See https://github.com/nanoporetech/medaka#models for more information. @@ -86,7 +86,7 @@ assembly: # assemblers used for shotgun sequencing with on Ion Torrent technology shotgun: "megahit-std" # assemblers used for amplicon sequencing with on Torrent technology - amplicon: "spades" + amplicon: "megahit-std" # minimum posterior probability for a clonal variant to be included in the generated pseudo-assembly min-variant-prob: 0.95 diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml index 151fb266..8501cab7 100644 --- a/workflow/envs/varlociraptor.yaml +++ b/workflow/envs/varlociraptor.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - varlociraptor =6.0 + - varlociraptor =8.4 From 33ac5f7b4f7af8bbb500e9f531ccbdc45ac9427f Mon Sep 17 00:00:00 2001 From: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Date: Wed, 15 Nov 2023 11:53:40 +0100 Subject: [PATCH 3/9] feat: Update README.md for dark/light theme (#614) * Update README.md for dark/light theme * Update README.md * Update README.md * Update README.md --- README.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0cbd7b4f..85ddca2b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,12 @@ # UnCoVar -![UnCoVar2](https://user-images.githubusercontent.com/77535027/133610563-d190e25c-504e-4953-92dd-f84a5b4a1191.png) + + + + + UnCoVar Logo dark/light + + ## SARS-CoV-2 Variant Calling and Lineage Assignment From 2bb74bfc26dee80af7d04089aafe636ea7c6d76a Mon Sep 17 00:00:00 2001 From: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Date: Wed, 15 Nov 2023 14:43:15 +0100 Subject: [PATCH 4/9] fix: QA genome generation (#613) * fix deprecated squeeze * fix wrong seq name * fmt * remove not needed file handling --- workflow/scripts/masking.py | 8 ++------ workflow/scripts/quality-filter.py | 8 +++----- 2 files changed, 5 insertions(+), 11 deletions(-) diff --git a/workflow/scripts/masking.py b/workflow/scripts/masking.py index 95fdb9d7..e02d4600 100644 --- a/workflow/scripts/masking.py +++ b/workflow/scripts/masking.py @@ -48,7 +48,6 @@ def get_base_count(pileupcolumn): for pileupread in pileupcolumn.pileups: # TODO Check pileupread for missing bases if not pileupread.is_del and not pileupread.is_refskip: - read_base = pileupread.alignment.query_sequence[pileupread.query_position] bases.append(read_base) @@ -102,7 +101,6 @@ def mask_sequence(sequence, coverages, base_counts): covered_postions = coverages.keys() for position, base in enumerate(sequence): - if position not in covered_postions: # TODO Check why there are postions that are not covered by any reads and are not Ns # sequence[position] = "N" @@ -160,10 +158,8 @@ def mask_sequence(sequence, coverages, base_counts): def write_sequence(sequence): - with pysam.FastxFile(snakemake.input.sequence) as infile, open( - snakemake.output.masked_sequence, mode="w" - ) as outfile: - print(">%s" % next(infile).name.split(".")[0], file=outfile) + with open(snakemake.output.masked_sequence, mode="w") as outfile: + print(">%s" % snakemake.wildcards.sample, file=outfile) print(sequence, file=outfile) diff --git a/workflow/scripts/quality-filter.py b/workflow/scripts/quality-filter.py index 7cc41b50..68977de2 100644 --- a/workflow/scripts/quality-filter.py +++ b/workflow/scripts/quality-filter.py @@ -31,13 +31,11 @@ def get_identity(quast_report_paths: List[str]) -> dict: sample = path.dirname(report_path).split("/")[-1] # load report - report_df = pd.read_csv( - report_path, delimiter="\t", index_col=0, squeeze=True, names=["value"] - ) - + report_df = pd.read_csv(report_path, delimiter="\t", names=["name", "value"]) + report_df.set_index("name", inplace=True) # select genome fraction (%) try: - fraction = float(report_df.at["Genome fraction (%)"]) / 100 + fraction = float(report_df.at["Genome fraction (%)", "value"]) / 100 except: # no "Genome fraction (%)" in quast report. Case for not assemblable samples fraction = 0.0 From 7f6146e925913480d26b600abd8815ae83127fad Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 16 Nov 2023 14:36:28 +0100 Subject: [PATCH 5/9] chore(deps): bump actions/checkout from 2 to 4 (#602) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: vBassewitz <104062464+vBassewitz@users.noreply.github.com> --- .github/workflows/copyright-preamble.yml | 2 +- .github/workflows/documentation.yml | 2 +- .github/workflows/main.yml | 10 +++++----- .github/workflows/release-please.yml | 4 ++-- .github/workflows/update-pangolin.yaml | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/copyright-preamble.yml b/.github/workflows/copyright-preamble.yml index 50aa610f..4005485f 100644 --- a/.github/workflows/copyright-preamble.yml +++ b/.github/workflows/copyright-preamble.yml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest steps: # Checking out the repository which is to be actioned - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 # Implementing action on repository - uses: VinnyBabuManjaly/copyright-action@v1.0.0 with: diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 226a47ce..2db38f85 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -18,7 +18,7 @@ jobs: deploy: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: SetUp Python uses: actions/setup-python@v4 diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 1dd78e03..728c2546 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -22,7 +22,7 @@ jobs: Formatting: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Formatting uses: github/super-linter@v5.0.0 env: @@ -39,7 +39,7 @@ jobs: env: GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Lint workflow uses: snakemake/snakemake-github-action@v1.24.0 with: @@ -55,7 +55,7 @@ jobs: # runs-on: ubuntu-latest # if: github.ref != 'refs/heads/master' # steps: - # - uses: actions/checkout@v2 + # - uses: actions/checkout@v4 # - uses: actions/setup-python@v4 # - uses: pre-commit/action@v3.0.0 @@ -75,7 +75,7 @@ jobs: # technology: [all, illumina, ion] seq_method: [shotgun, amplicon] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - uses: actions/setup-python@v4 with: python-version: '3.11' @@ -192,7 +192,7 @@ jobs: ] # generate_test_cases, steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 # - name: Cache conda dependencies # uses: actions/cache@v2 diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml index 2c4b823d..0f2ca659 100644 --- a/.github/workflows/release-please.yml +++ b/.github/workflows/release-please.yml @@ -68,14 +68,14 @@ jobs: remove-android: "true" - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Space run: | echo "Free space:" df -h - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Checkout release PR locally if: ${{ steps.pr_created.outputs.pr == 'true' && steps.release.outputs.release_created != 'true' }} diff --git a/.github/workflows/update-pangolin.yaml b/.github/workflows/update-pangolin.yaml index 99a9e4b5..736c8fd1 100644 --- a/.github/workflows/update-pangolin.yaml +++ b/.github/workflows/update-pangolin.yaml @@ -9,7 +9,7 @@ jobs: Create-PR-for-new-Pangolin-release: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Install mamba uses: conda-incubator/setup-miniconda@v2 From b986b20b226a0bae74cec0cbe815892b20debe5f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 16 Nov 2023 17:09:14 +0100 Subject: [PATCH 6/9] chore(deps): bump khan/pull-request-workflow-cancel from 1.0.0 to 1.0.1 (#580) Bumps [khan/pull-request-workflow-cancel](https://github.com/khan/pull-request-workflow-cancel) from 1.0.0 to 1.0.1. - [Release notes](https://github.com/khan/pull-request-workflow-cancel/releases) - [Commits](https://github.com/khan/pull-request-workflow-cancel/compare/1.0.0...1.0.1) --- updated-dependencies: - dependency-name: khan/pull-request-workflow-cancel dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: vBassewitz <104062464+vBassewitz@users.noreply.github.com> --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 728c2546..ea3320a8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest if: github.ref != 'refs/heads/master' steps: - - uses: khan/pull-request-workflow-cancel@1.0.0 + - uses: khan/pull-request-workflow-cancel@1.0.1 with: workflows: "main.yml" env: From ed041c832987f014e267a85686465b1ac469fa11 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 17 Nov 2023 10:13:44 +0100 Subject: [PATCH 7/9] chore(master): release 0.16.0 (#586) * chore(master): release 0.16.0 * Changed containerized tag to 0.16.0 --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] Co-authored-by: vBassewitz <104062464+vBassewitz@users.noreply.github.com> --- CHANGELOG.md | 23 +++++++++++++++++++++++ version.txt | 2 +- workflow/Snakefile | 2 +- 3 files changed, 25 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ac27577d..5f16dd03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,28 @@ # Changelog +## [0.16.0](https://github.com/IKIM-Essen/uncovar/compare/v0.15.1...v0.16.0) (2023-11-16) + + +### Features + +* Update README.md for dark/light theme ([#614](https://github.com/IKIM-Essen/uncovar/issues/614)) ([33ac5f7](https://github.com/IKIM-Essen/uncovar/commit/33ac5f7b4f7af8bbb500e9f531ccbdc45ac9427f)) + + +### Bug Fixes + +* changes in path requirements for snakedeploy ([#590](https://github.com/IKIM-Essen/uncovar/issues/590)) ([406d456](https://github.com/IKIM-Essen/uncovar/commit/406d456edd15715f7e14338b8195d2a09a807e49)) +* improved clonality event definition, usage of major subclone for assembly polishing; upgrade to varlociraptor 6.0 ([#585](https://github.com/IKIM-Essen/uncovar/issues/585)) ([aced95e](https://github.com/IKIM-Essen/uncovar/commit/aced95e798fd0483e99120550f49614e680f56dd)) +* QA genome generation ([#613](https://github.com/IKIM-Essen/uncovar/issues/613)) ([2bb74bf](https://github.com/IKIM-Essen/uncovar/commit/2bb74bfc26dee80af7d04089aafe636ea7c6d76a)) +* switch from jupyter notebook to script ([#598](https://github.com/IKIM-Essen/uncovar/issues/598)) ([d0f293d](https://github.com/IKIM-Essen/uncovar/commit/d0f293d2b8136fb0d8ef3753733ab1d30fb20d56)) +* update multiqc ([#607](https://github.com/IKIM-Essen/uncovar/issues/607)) ([0070d89](https://github.com/IKIM-Essen/uncovar/commit/0070d8927290dd01f418b876b60f3405158f1ab9)) +* use homopolymer-pair-HMM-mode of Varlociraptor in case of nanopore reads ([505a271](https://github.com/IKIM-Essen/uncovar/commit/505a2714ba0e5642312051f5e5154f7d454ff57f)) +* use homopolymer-pair-HMM-mode of Varlociraptor in case of nanopore reads ([#587](https://github.com/IKIM-Essen/uncovar/issues/587)) ([9bc814f](https://github.com/IKIM-Essen/uncovar/commit/9bc814f7cb9e9d9e53d557d463e782801070b46e)) + + +### Performance Improvements + +* update to varlociraptor 8.4 ([#596](https://github.com/IKIM-Essen/uncovar/issues/596)) ([34701af](https://github.com/IKIM-Essen/uncovar/commit/34701af485aa1ec199a418ec1487a97677f624ca)) + ## [0.15.1](https://github.com/IKIM-Essen/uncovar/compare/v0.15.0...v0.15.1) (2022-11-30) diff --git a/version.txt b/version.txt index e815b861..04a373ef 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -0.15.1 +0.16.0 diff --git a/workflow/Snakefile b/workflow/Snakefile index d8f339ce..cd146b36 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -21,7 +21,7 @@ report: "report/workflow.rst" container: "docker://condaforge/mambaforge" -containerized: "quay.io/uncovar/uncovar#0.15.1" +containerized: "quay.io/uncovar/uncovar#0.16.0" include: "rules/common.smk" From d87c9ad42cd295f429b5e5f8d17fba1ad7d11e60 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 17 Nov 2023 14:17:16 +0100 Subject: [PATCH 8/9] chore(deps): bump peter-evans/create-pull-request from 4 to 5 (#592) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: vBassewitz <104062464+vBassewitz@users.noreply.github.com> --- .github/workflows/copyright-preamble.yml | 2 +- .github/workflows/update-pangolin.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/copyright-preamble.yml b/.github/workflows/copyright-preamble.yml index 4005485f..dae852ee 100644 --- a/.github/workflows/copyright-preamble.yml +++ b/.github/workflows/copyright-preamble.yml @@ -25,7 +25,7 @@ jobs: # Creates pull request with all changes in file - name: Create Pull Request - uses: peter-evans/create-pull-request@v4 + uses: peter-evans/create-pull-request@v5 with: commit-message: "chore: update copyright preamble" delete-branch: true diff --git a/.github/workflows/update-pangolin.yaml b/.github/workflows/update-pangolin.yaml index 736c8fd1..bdb8d055 100644 --- a/.github/workflows/update-pangolin.yaml +++ b/.github/workflows/update-pangolin.yaml @@ -37,7 +37,7 @@ jobs: - name: Create Pull Request if: ${{ env.LATEST_PANGOLIN != env.CURRENT_PANGOLIN }} id: cpr - uses: peter-evans/create-pull-request@v4 + uses: peter-evans/create-pull-request@v5 with: token: ${{ secrets.GITHUB_TOKEN }} committer: GitHub From 4b2f34c54b522152f402112b7d82c42d6c95b95d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 17 Nov 2023 16:07:09 +0100 Subject: [PATCH 9/9] chore(deps): bump docker/build-push-action from 3 to 5 (#599) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 3 to 5. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/v3...v5) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: vBassewitz <104062464+vBassewitz@users.noreply.github.com> --- .github/workflows/release-please.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml index 0f2ca659..ad185be4 100644 --- a/.github/workflows/release-please.yml +++ b/.github/workflows/release-please.yml @@ -140,7 +140,7 @@ jobs: - name: Build and push if: ${{ steps.release.outputs.release_created == 'true' }} - uses: docker/build-push-action@v3 + uses: docker/build-push-action@v5 with: context: . push: true