Merge pull request #497 from bactopia/dev

update bactopia to v3.0.1
bactopia · Mar 25, 2024 · 0c13e71 · 0c13e71
2 parents 89885c5 + 3ce8c53
commit 0c13e71
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diff --git a/.github/workflows/all-bactopia-tests.yml b/.github/workflows/all-bactopia-tests.yml
@@ -14,7 +14,7 @@ jobs:
 
     steps:
       - name: Checkout bactopia/bactopia
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           path: ${{ github.run_id }}/bactopia
 
@@ -26,40 +26,48 @@ jobs:
           echo "BACTOPIA_TESTS=/data/storage/bactopia-ci/bactopia-tests/data" >> $GITHUB_ENV
           echo "BACTOPIA_WORKSPACE=${GITHUB_WORKSPACE}/${{ github.run_id }}/bactopia" >> $GITHUB_ENV
           echo "BACTOPIA_TMP=/data/storage/bactopia-tmp/${{ github.run_id }}" >> $GITHUB_ENV
-          mkdir "/data/storage/bactopia-tmp/${{ github.run_id }}"
+          echo "NXF_SINGULARITY_CACHEDIR=/data/storage/bactopia-ci/envs/singularity" >> $GITHUB_ENV
+          echo "NXF_SINGULARITY_HOME_MOUNT=true" >> $GITHUB_ENV
+          echo "SINGULARITY_CACHEDIR=/data/storage/bactopia-ci/envs/singularity" >> $GITHUB_ENV
+          echo "SINGULARITY_TMPDIR=/data/storage/bactopia-tmp/${{ github.run_id }}/tmp" >> $GITHUB_ENV
+          echo "TMP=/data/storage/bactopia-tmp/${{ github.run_id }}/tmp" >> $GITHUB_ENV
+          echo "TMPDIR=/data/storage/bactopia-tmp/${{ github.run_id }}/tmp" >> $GITHUB_ENV
+          mkdir -p "/data/storage/bactopia-tmp/${{ github.run_id }}/tmp"
+          chmod -R 777 "/data/storage/bactopia-tmp/${{ github.run_id }}"
 
-      - name: Conda Profile
+      - name: Singularity Profile
         run: |
-          source /data/storage/bactopia-ci/mambaforge/etc/profile.d/conda.sh
+          source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh
           conda activate bactopia-ci
           cd ${{ env.BACTOPIA_WORKSPACE }}
-          ls modules/local/bactopia | xargs -I {} -P 10 -n 1\
-              bash -c 'BACTOPIA_ARGS="-profile test --condadir ${{ env.BACTOPIA_CONDA }} --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
-                       pytest --wt 10 --symlink --kwdof -o "testpaths=tests modules/local/bactopia" --git-aware --tag {}'
+          ls subworkflows/local/ | grep -v -E "teton|srahumanscrubber" | xargs -I {} -P 20 \
+              bash -c 'BACTOPIA_ARGS="-profile singularity --singularity_pull_docker_container --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
+                       pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}'
 
       - name: Docker Profile
         run: |
-          source /data/storage/bactopia-ci/mambaforge/etc/profile.d/conda.sh
+          source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh
           conda activate bactopia-ci
           cd ${{ env.BACTOPIA_WORKSPACE }}
-          ls modules/local/bactopia | xargs -I {} -P 10 -n 1\
-              bash -c 'BACTOPIA_ARGS="-profile test,docker --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
-                       pytest --wt 10 --symlink --kwdof -o "testpaths=tests modules/local/bactopia" --git-aware --tag {}'
+          ls subworkflows/local/ | grep -v -E "teton|srahumanscrubber" | xargs -I {} -P 20 \
+              bash -c 'BACTOPIA_ARGS="-profile docker --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
+                       pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}'
 
-      - name: Singularity Profile
+      - name: Conda Profile
         run: |
-          source /data/storage/bactopia-ci/mambaforge/etc/profile.d/conda.sh
+          source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh
           conda activate bactopia-ci
+          conda clean --all -y
           cd ${{ env.BACTOPIA_WORKSPACE }}
-          ls modules/local/bactopia | xargs -I {} -P 10 -n 1\
-              bash -c 'BACTOPIA_ARGS="-profile test,singularity --singularity_cache ${{ env.BACTOPIA_SINGULARITY }} --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
-                       pytest --wt 10 --symlink --kwdof -o "testpaths=tests modules/local/bactopia" --git-aware --tag {}'
+          ls subworkflows/local/ | grep -v -E "teton|srahumanscrubber" | xargs -I {} -P 20 \
+              bash -c 'BACTOPIA_ARGS="--is_ci --condadir ${{ env.BACTOPIA_CONDA }} --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
+                       pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}'
 
       - name: Upload logs on failure
         if: failure()
         uses: actions/upload-artifact@v2
         with:
-          name: logs-bactopia
+          name: logs-bactopia-tools
           path: |
             ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.out
             ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.err
@@ -69,8 +77,7 @@ jobs:
             ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.out
             ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stderr.txt
             ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stdout.txt
-            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*versions.yml
-           
+            
       - name: Cleanup
         if: always()
         run: rm -rf ${GITHUB_WORKSPACE}/${{ github.run_id }} ${{ env.BACTOPIA_TMP }}
diff --git a/.github/workflows/all-bactopia-tool-tests.yml b/.github/workflows/all-bactopia-tool-tests.yml
diff --git a/.github/workflows/conda-build-manual.yml b/.github/workflows/conda-build-manual.yml
@@ -15,19 +15,18 @@ jobs:
         with:
           ref: dev
 
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           activate-environment: anaconda-client-env
-          use-mamba: true
 
       - name: Build and Push 
         run: |
           # Start build
           conda install -c conda-forge -c bioconda anaconda-client conda-build conda-verify
-          cd data/conda/ && mamba build -c conda-forge -c bioconda -c defaults --output-folder . . 
+          cd data/conda/ && conda build -c conda-forge -c bioconda -c defaults --output-folder . . 
           anaconda upload --force ./noarch/*.tar.bz2
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -3,8 +3,17 @@
         "master"
     ],
     "cSpell.words": [
+        "bakta",
         "btype",
+        "CACHEDIR",
+        "cleanyerreads",
+        "getenv",
         "infodir",
-        "subdir"
+        "nfconfig",
+        "println",
+        "prokka",
+        "staphopia",
+        "subdir",
+        "Subworkflow"
     ]
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,57 @@ description: A full list of Bactopia releases and a description of the changes.
 ---
 # Changelog
 
+## v3.0.1 bactopia/bactopia "That's My Girl" - 2024/03/25
+
+### `Added`
+
+- Updated `bactopia-assembler` to include updated Medaka models
+- profile for `arcc_hawk`
+- TB Profiler results are now merged with `collate` command
+- sample name to plasmidfinder results
+- support config files from nf-core/configs
+- updated AMRFinder+ database for v3.12.8
+- bump program versions in modules
+    - `abritamr`: 1.0.14 -> 1.0.17
+    - `bactopia-assembler`: 1.0.3 -> 1.0.4
+    - `bactopia-teton`: 1.0.1 -> 1.0.2
+    - `bactopia-variants`: 1.0.1 -> 1.0.2
+    - `bakta`: 1.8.2 -> 1.9.3
+    - `blast`: 2.14.1 -> 2.15.0
+    - `busco`: 5.5.0 -> 5.7.0
+    - `gubbins`: 3.3.0 -> 3.3.4
+    - `multiqc`: 1.15 -> 1.21
+    - `mashtree`: 1.4.5 -> 1.4.6
+    - `mykrobe`: 0.12.2 -> 0.13.0
+    - `ncbi-amrfinderplus`: 3.11.18 -> 3.12.8
+    - `panaroo`: 1.3.3 -> 1.4.2
+    - `rgi`: 6.0.2 -> 6.0.3
+    - `sistr`: 1.1.1 -> 1.1.2
+    - `stecfinder`: 1.1.0 -> 1.1.1
+    - `tbprofiler`: 5.0.0 -> 6.1.0
+
+### `Fixed`
+
+- variable name in sketcher module
+- `--para-off` not correctly implemented in PIRATE module
+- extra space in RGI container image name
+- sourmash version STDERR not parsed out
+- FASTQC writing to /tmp dir on HPC when non-readable
+- abricate and ariba not using output subdirectory
+- nextflow tower typos @iferres
+- phispy not working with Bakta genbank files
+- missed check of `--download_bakta` param in main workflow
+- quast not working when estimated genome size is 0
+- `abricate` now gets database subdirectories
+
+### `Enhancements to OSS`
+
+- fix amrfinderplus pinning in abritamr [bioconda/bioconda-recipes#46714](https://github.com/bioconda/bioconda-recipes/pull/46714)
+- adjust python pinning in gubbins [bioconda/bioconda-recipes#46713](https://github.com/bioconda/bioconda-recipes/pull/46713)
+- fix issue with sistr container [bioconda/bioconda-recipes#46712](https://github.com/bioconda/bioconda-recipes/pull/46712)
+- update rgi pinning for pyrodigal [bioconda/bioconda-recipes#46669](https://github.com/bioconda/bioconda-recipes/pull/46669)
+- pin tabix version in snippy [bioconda/bioconda-recipes#46458](https://github.com/bioconda/bioconda-recipes/pull/46458)
+
 ## v3.0.0 bactopia/bactopia "Black Cat and Brown Dog" - 2023/09/11
 
 ### `Added`