Merge branch 'master' into refactor/docs-exec

IKIM-Essen · Nov 5, 2024 · 19d21ba · 19d21ba
2 parents 68ed1ed + 17b4f32
commit 19d21ba
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diff --git a/.github/workflows/check-todos.yml b/.github/workflows/check-todos.yml
@@ -11,4 +11,4 @@ jobs:
     steps:
       - uses: "actions/checkout@master"
       - name: "TODO to Issue"
-        uses: "alstr/todo-to-issue-action@v4.13"
+        uses: "alstr/todo-to-issue-action@v5"
diff --git 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@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           commit-message: "chore: update copyright preamble"
           delete-branch: true

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -23,8 +23,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: Formatting
-        uses: super-linter/super-linter@v5.7.2
+        uses: super-linter/super-linter@v7.1.0
         env:
           VALIDATE_ALL_CODEBASE: false
           DEFAULT_BRANCH: master
@@ -64,7 +66,6 @@ jobs:
     env:
       GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
     needs:
-      - Formatting
       - Linting
       #- Pre-Commit
     strategy:
@@ -179,7 +180,7 @@ jobs:
         uses: actions/upload-artifact@v4
         if: matrix.technology == 'all' && matrix.rule != 'all -npr'
         with:
-          name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }}
+          name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }}-${{ matrix.seq_method }}
           path: .tests/logs/
 
       - name: Change permissions for caching
@@ -193,7 +194,6 @@ jobs:
     env:
       GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
     needs:
-      - Formatting
       - Linting
       #- Pre-Commit
     strategy:
@@ -203,7 +203,6 @@ jobs:
             benchmark_strain_calling,
             benchmark_assembly,
             benchmark_mixtures,
-            benchmark_non_sars_cov_2,
             benchmark_reads,
             compare_assemblers,
           ]

diff --git 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@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true

diff --git 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@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           committer: GitHub <[email protected]>

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,27 @@
 # Changelog
 
+## [1.1.1](https://github.com/IKIM-Essen/uncovar/compare/v1.1.0...v1.1.1) (2024-11-04)
+
+
+### Bug Fixes
+
+* fix file not found error on shared fs storage ([#673](https://github.com/IKIM-Essen/uncovar/issues/673)) ([c28db96](https://github.com/IKIM-Essen/uncovar/commit/c28db9608c816cc775397096d45bd33c8e59aace))
+
+## [1.1.0](https://github.com/IKIM-Essen/uncovar/compare/v1.0.0...v1.1.0) (2024-10-31)
+
+
+### Features
+
+* FLiRT Mutations column ([#664](https://github.com/IKIM-Essen/uncovar/issues/664)) ([f77d42e](https://github.com/IKIM-Essen/uncovar/commit/f77d42e2154a95b6ca0e2c127df8ca134eda1789))
+
+
+### Bug Fixes
+
+* changed kraken input files for ont ([#650](https://github.com/IKIM-Essen/uncovar/issues/650)) ([b62007c](https://github.com/IKIM-Essen/uncovar/commit/b62007c7b10b9d933528a6b02933cca4bd751100))
+* move primer file location under workflow; this avoids file not being found in shared filesystems ([#665](https://github.com/IKIM-Essen/uncovar/issues/665)) ([9cb1576](https://github.com/IKIM-Essen/uncovar/commit/9cb1576a8c41c23344940f2248e5d44464a53b2e))
+* pangolin data updates ([#662](https://github.com/IKIM-Essen/uncovar/issues/662)) ([f46ec83](https://github.com/IKIM-Essen/uncovar/commit/f46ec833ed56c39820c0a0e8d8e0295050a334ab))
+* replace ragoo with ragtag ([#591](https://github.com/IKIM-Essen/uncovar/issues/591)) ([e64e9db](https://github.com/IKIM-Essen/uncovar/commit/e64e9db7e81a295ff1775b880c255b71274448fd))
+
 ## [1.0.0](https://github.com/IKIM-Essen/uncovar/compare/v0.16.0...v1.0.0) (2024-04-17)
 
 

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-1.0.0
+1.1.1
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -21,7 +21,7 @@ report: "report/workflow.rst"
 container: "docker://condaforge/mambaforge"
 
 
-containerized: "quay.io/uncovar/uncovar#1.0.0"
+containerized: "quay.io/uncovar/uncovar#1.1.1"
 
 
 include: "rules/common.smk"

diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml
@@ -4,3 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - pangolin =4.3
+  - snakemake-minimal=7.24.0 # TODO keep until https://github.com/bioconda/bioconda-recipes/pull/42192 and we can pin to 4.3.1 above
diff --git a/workflow/envs/ragoo.yaml → workflow/envs/ragtag.yaml b/workflow/envs/ragoo.yaml → workflow/envs/ragtag.yaml
@@ -4,4 +4,4 @@ channels:
   - imperial-college-research-computing
   - nodefaults
 dependencies:
-  - ragoo =1.1
+  - ragtag =2.1
diff --git a/workflow/envs/spades.yaml b/workflow/envs/spades.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - spades =3.15
+  - spades =4.0
diff --git a/workflow/report/assembly_illumina.rst b/workflow/report/assembly_illumina.rst
@@ -1,3 +1,3 @@
 Assembly of sample {{ snakemake.wildcards.sample }}.
-Reads were assembled with {{ "`metaSPAdes <https://github.com/ablab/spades>`_" if snakemake.params.is_amp else "`Megahit <https://github.com/voutcn/megahit>`_" }}, followed by reference based contig ordering and concatenation with `RaGOO <https://github.com/malonge/RaGOO>`_.
+Reads were assembled with {{ "`metaSPAdes <https://github.com/ablab/spades>`_" if snakemake.params.is_amp else "`Megahit <https://github.com/voutcn/megahit>`_" }}, followed by reference based contig ordering and concatenation with `RagTag <https://github.com/malonge/RagTag>`_.
 Then, assembly was polished by applying variants with an allele frequency of 100% (called by `Varlociraptor <https://varlociraptor.github.io>`_ at FDR 5%).
diff --git a/workflow/report/assembly_ont.rst b/workflow/report/assembly_ont.rst
@@ -1,2 +1,2 @@
 Assembly of sample {{ snakemake.wildcards.sample }}.
-Reads were assembled with `SPAdes <https://github.com/ablab/spades>`_, followed by reference based contig ordering and concatenation with `RaGOO <https://github.com/malonge/RaGOO>`_.
+Reads were assembled with `SPAdes <https://github.com/ablab/spades>`_, followed by reference based contig ordering and concatenation with `RagTag <https://github.com/malonge/RagTag>`_.
diff --git a/workflow/report/qc-report.rst b/workflow/report/qc-report.rst
@@ -1,3 +1,3 @@
 QC overview for samples from {{ snakemake.wildcards.date }}.
-Readcounts for raw, trimmed and filtered reads, length of initially assembled (`Megahit <https://github.com/voutcn/megahit>`_/`metaSPAdes <https://github.com/ablab/spades>`_) and reference ordered contigs (`RaGOO <https://github.com/malonge/RaGOO>`_).
+Readcounts for raw, trimmed and filtered reads, length of initially assembled (`Megahit <https://github.com/voutcn/megahit>`_/`metaSPAdes <https://github.com/ablab/spades>`_) and reference ordered contigs (`RagTag <https://github.com/malonge/RagTag>`_).
 Percentil overview for contamination in the raw reads (`kraken <https://github.com/DerrickWood/kraken>`_) and called COVID-19-strain including defining SNPs (`Pangolin <https://github.com/cov-lineages/pangolin>`_) and variants of interest from variant calling (`Varlociraptor <https://varlociraptor.github.io>`_).
diff --git a/workflow/resources/nCoV-2019.primer.bed b/workflow/resources/nCoV-2019.primer.bed
@@ -0,0 +1,218 @@
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