Merge branch 'master' into dependabot/github_actions/khan/pull-reques…

…t-workflow-cancel-1.0.1
IKIM-Essen · Nov 16, 2023 · d7e2858 · d7e2858
2 parents 3babc1c + 7f6146e
commit d7e2858
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diff --git 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/[email protected]
         with:

diff --git 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
@@ -22,9 +22,9 @@ jobs:
   Formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Formatting
-        uses: github/super-linter@v4.10.1
+        uses: github/super-linter@v5.0.0
         env:
           VALIDATE_ALL_CODEBASE: false
           DEFAULT_BRANCH: master
@@ -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/[email protected]
         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/[email protected]
 
@@ -71,11 +71,14 @@ jobs:
       matrix:
         rule: [all, all -npr]
         # disable ont actions
-        # technology: [all, illumina, ont, ion]
-        technology: [all, illumina, ion]
+        technology: [all, illumina, ont, ion]
+        # 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'
 
       # android - will release about 10 GB if you don't need Android
       # dotnet  - will release about 20 GB if you don't need .NET
@@ -103,14 +106,14 @@ jobs:
           curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.2.fastq.gz
           echo sample_name,fq1,fq2,date,is_amplicon_data,technology > .tests/config/pep/samples.csv
           echo illumina-test,data/B117.1.fastq.gz,data/B117.2.fastq.gz,2022-01-01,$AMPLICON,illumina >> .tests/config/pep/samples.csv
-      # - name: Prepare test data for Oxford Nanopore
-      #   if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ont' || matrix.rule == 'compare_assemblers')
-      #   run: |
-      #     if [[ "${{ matrix.seq_method }}"  = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi
-      #     mkdir -p .tests/data
-      #     curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ont_reads.fastq.gz > .tests/data/ont_reads.fastq.gz
-      #     echo sample_name,fq1,date,is_amplicon_data,technology > .tests/config/pep/samples.csv
-      #     echo ont-test,data/ont_reads.fastq.gz,2022-01-01,$AMPLICON,ont >> .tests/config/pep/samples.csv
+      - name: Prepare test data for Oxford Nanopore
+        if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ont' || matrix.rule == 'compare_assemblers')
+        run: |
+          if [[ "${{ matrix.seq_method }}"  = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi
+          mkdir -p .tests/data
+          curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ont_reads.fastq.gz > .tests/data/ont_reads.fastq.gz
+          echo sample_name,fq1,date,is_amplicon_data,technology > .tests/config/pep/samples.csv
+          echo ont-test,data/ont_reads.fastq.gz,2022-01-01,$AMPLICON,ont >> .tests/config/pep/samples.csv
       - name: Prepare test data for Ion Torrent
         if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ion' || matrix.rule == 'compare_assemblers')
         run: |
@@ -189,7 +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
@@ -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' }}
@@ -128,7 +128,7 @@ jobs:
 
       - name: Set up Docker Buildx
         if: ${{ steps.release.outputs.release_created == 'true' }}
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to Quay Registry
         if: ${{ steps.release.outputs.release_created == 'true' }}

diff --git 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

diff --git 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)
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://github.com/IKIM-Essen/uncovar/assets/77535027/8e17c6fc-ff7a-4c25-afc9-7888036d693e">
+  <source media="(prefers-color-scheme: light)" srcset="https://github.com/IKIM-Essen/uncovar/assets/77535027/c99f5a94-749b-422e-b319-1e3700d40a8e">
+  <img alt="UnCoVar Logo dark/light">
+</picture>
+
 
 ## SARS-CoV-2 Variant Calling and Lineage Assignment
 

diff --git 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/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
diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - varlociraptor =5.3
+  - varlociraptor =8.4
diff --git a/workflow/notebooks/assembly-benchmark-results.py.ipynb b/workflow/notebooks/assembly-benchmark-results.py.ipynb
diff --git a/workflow/rules/assembly.smk b/workflow/rules/assembly.smk
@@ -159,8 +159,8 @@ rule filter_chr0:
 rule assembly_polishing_illumina:
     input:
         fasta="results/{date}/contigs/ordered/{sample}.fasta",
-        bcf="results/{date}/filtered-calls/ref~{sample}/{sample}.clonal.nofilter.orf.bcf",
-        bcfidx="results/{date}/filtered-calls/ref~{sample}/{sample}.clonal.nofilter.orf.bcf.csi",
+        bcf="results/{date}/filtered-calls/ref~{sample}/{sample}.subclonal-major.nofilter.orf.bcf",
+        bcfidx="results/{date}/filtered-calls/ref~{sample}/{sample}.subclonal-major.nofilter.orf.bcf.csi",
     output:
         report(
             "results/{date}/polishing/bcftools-illumina/{sample}.fasta",