Merge branch 'master' into fc-dnaapler

StaPH-B · Nov 25, 2024 · a50f04a · a50f04a
2 parents 586cf8a + ba922fd
commit a50f04a
Show file tree

Hide file tree

Showing 108 changed files with 6,512 additions and 44 deletions.
diff --git a/.github/workflows/run-singularity.yml b/.github/workflows/run-singularity.yml
@@ -20,15 +20,15 @@ on:
 jobs:
 
   build_singularity:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Check out Repo
         uses: actions/checkout@v4
 
       - name: Set up Singularity
-        uses: eWaterCycle/setup-singularity@v7
+        uses: eWaterCycle/setup-apptainer@v2
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.5
 
-      - name: Run a singularity container
-        run: singularity run docker://${{ inputs.repository_name }}/${{ inputs.image_name }} ${{ inputs.command }}
+      - name: Run a singularity/apptainer container
+        run: apptainer run docker://${{ inputs.repository_name }}/${{ inputs.image_name }} ${{ inputs.command }}
diff --git a/.github/workflows/update_freyja.yml b/.github/workflows/update_freyja.yml
@@ -9,7 +9,7 @@ name: Update Freyja
 on: 
   workflow_dispatch:
   schedule:
-    - cron: '30 7 1 * *'
+    - cron: '30 7 * * 1'
 
 run-name: Updating Freyja
 
@@ -23,7 +23,7 @@ jobs:
       - name: set freyja version
         id: latest_version
         run: |
-          version=1.5.1
+          version=1.5.2
           echo "version=$version" >> $GITHUB_OUTPUT 
           
           file=freyja/$version/Dockerfile

diff --git a/.github/workflows/update_pango_aliasor.yml b/.github/workflows/update_pango_aliasor.yml
@@ -0,0 +1,82 @@
+##### ------------------------------------------------------------------------------------------------ #####
+##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most   #####
+##### recent version of pango_aliasor and downloads the current pangolin lineages.                     #####
+##### It takes no manual input.                                                                        #####
+##### ------------------------------------------------------------------------------------------------ #####
+
+name: Update pango aliasor
+
+on: 
+  workflow_dispatch:
+  schedule:
+    - cron: '30 7 * * 1'
+
+run-name: Updating pango aliasor
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: pull repo
+        uses: actions/checkout@v4
+
+      - name: set pango_aliasor version
+        id: latest_version
+        run: |
+          version=0.3.0
+          echo "version=$version" >> $GITHUB_OUTPUT 
+          
+          file=pango_aliasor/0.3.0/Dockerfile
+          ls $file
+          echo "file=$file" >> $GITHUB_OUTPUT
+
+      - name: set up docker buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: build to test
+        id: docker_build_to_test
+        uses: docker/build-push-action@v5
+        with:
+          context: pango_aliasor/${{ steps.latest_version.outputs.version }}
+          target: test
+          load: true
+          push: false
+          tags: pango_aliasor:update
+
+      - name: Get current date
+        id: date
+        run: |
+          date=$(date '+%Y-%m-%d')
+          echo "the date is $date"
+          echo "date=$date" >> $GITHUB_OUTPUT
+      
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Login to Quay
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
+
+      - name: Build and push user-defined tag to DockerHub
+        id: docker_build_user_defined_tag
+        uses: docker/build-push-action@v5
+        with:
+          file: ${{ steps.latest_version.outputs.file }}
+          target: app
+          push: true
+          tags: |
+            staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
+            staphb/pango_aliasor:latest
+            quay.io/staphb/pango_aliasor:${{ steps.latest_version.outputs.version }}-${{ steps.date.outputs.date }}
+            quay.io/staphb/pango_aliasor:latest
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
diff --git a/Program_Licenses.md b/Program_Licenses.md
@@ -13,6 +13,7 @@ The licenses of the open-source software that is contained in these Docker image
 | artic-ncov2019-epi2me | MPL 2.0 | https://github.com/epi2me-labs/wf-artic/blob/master/LICENSE |
 | any2fasta | GNU GPLv3 | https://github.com/tseemann/any2fasta/blob/master/LICENSE |
 | ARIBA | GNU GPLv3 | https://github.com/sanger-pathogens/ariba/blob/master/LICENSE |
+| assembly_snptyper | MIT | https://github.com/boasvdp/assembly_snptyper/blob/main/LICENSE |
 | Augur | GNU Affero GPLv3 | https://github.com/nextstrain/augur/blob/master/LICENSE.txt |
 | Auspice | GNU Affero GPLv3 | https://github.com/nextstrain/auspice/blob/master/LICENSE.txt |
 | Bakta | GNU GPLv3 | https://github.com/oschwengers/bakta/blob/main/LICENSE |
@@ -30,6 +31,8 @@ The licenses of the open-source software that is contained in these Docker image
 | CDC-SPN | GitHub No License | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
 | cfsan-snp-pipeline | non-standard license see --> | https://github.com/CFSAN-Biostatistics/snp-pipeline/blob/master/LICENSE.txt |
 | CheckM | GNU GPLv3 | https://github.com/Ecogenomics/CheckM/blob/master/LICENSE |
+| CheckM2 | GNU GPLv3 | https://github.com/chklovski/CheckM2/blob/main/LICENSE |
+| CheckV | MIT | https://bitbucket.org/berkeleylab/checkv/src/master/LICENSE.txt |
 | Circlator | GNU GPLv3 | https://github.com/sanger-pathogens/circlator/blob/master/LICENSE |
 | Circos | GNU GPLv3 | https://circos.ca/ |
 | CirculoCov | GNU GPLv3 | https://github.com/erinyoung/CirculoCov/blob/main/LICENSE |
@@ -38,6 +41,7 @@ The licenses of the open-source software that is contained in these Docker image
 | datasets-sars-cov-2 | Apache 2.0 | https://github.com/CDCgov/datasets-sars-cov-2/blob/master/LICENSE |
 | diamond | GNU GPLv3 | https://github.com/bbuchfink/diamond/blob/master/LICENSE |
 | dnaapler | MIT | https://github.com/gbouras13/dnaapler/blob/main/LICENSE |
+| dorado | Oxford Nanopore Technologies PLC Public License | [ONT License](https://github.com/nanoporetech/dorado/blob/master/LICENCE.txt) |
 | dragonflye | GNU GPLv3 | https://github.com/rpetit3/dragonflye/blob/main/LICENSE |
 | drprg | MIT | https://github.com/mbhall88/drprg/blob/main/LICENSE |
 | DSK | GNU Affero GPLv3 | https://github.com/GATB/dsk/blob/master/LICENSE |
@@ -69,6 +73,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Hmmer | BSD-3 | http://eddylab.org/software/hmmer/Userguide.pdf |
 | homopolish | GNU GPLv3 | https://github.com/ythuang0522/homopolish/blob/master/LICENSE |
 | htslib | MIT | https://github.com/samtools/htslib/blob/develop/LICENSE |
+| Integron Finder | GNU GPLv3 | https://github.com/gem-pasteur/Integron_Finder/blob/master/COPYING |
 | iqtree | GNU GPLv2 | https://github.com/Cibiv/IQ-TREE/blob/master/LICENSE |
 | iqtree2 | GNU GPLv2 | https://github.com/iqtree/iqtree2/blob/master/LICENSE |
 | IPA | BSD-3 | https://github.com/PacificBiosciences/pbipa/blob/master/LICENSE.txt |
@@ -81,6 +86,7 @@ The licenses of the open-source software that is contained in these Docker image
 | kma | Apache v2.0 | https://bitbucket.org/genomicepidemiology/kma/src/master/ |
 | Kraken | GNU GPLv3 | https://github.com/DerrickWood/kraken/blob/master/LICENSE |
 | Kraken2 | MIT | https://github.com/DerrickWood/kraken2/blob/master/LICENSE |
+| KrakenTools | GNU GPLv3 | https://github.com/jenniferlu717/KrakenTools/blob/master/LICENSE |
 | KrakenUniq | GNU GPLv3 | https://github.com/fbreitwieser/krakenuniq/blob/master/LICENSE |
 | kSNP3 | BSD | available in zipped kSNP archive on sourceforge or in docker image under `/kSNP3.1_Linux_package/THE BSD OPENSOURCE LICENSE.pdf` |
 | kSNP4 | BSD | available in zipped kSNP archive on sourceforge or in docker image under `/opt/kSNP4 Linux package/Documentation/THE BSD OPENSOURCE LICENSE.pdf` |
@@ -151,6 +157,7 @@ The licenses of the open-source software that is contained in these Docker image
 | SalmID| MIT | https://github.com/hcdenbakker/SalmID/blob/master/LICENSE |
 | samclip | GNU GPLv3 | https://github.com/tseemann/samclip/blob/master/LICENSE |
 | Samtools | GNU GPLv3 | https://github.com/samtools/samtools/blob/develop/LICENSE |
+| SeqFu | GNU GPLv3 | https://github.com/telatin/seqfu2 |
 | SeqKit | MIT | https://github.com/shenwei356/seqkit/blob/master/LICENSE
 | SeqSero | GNU GPLv2 | https://github.com/denglab/SeqSero/blob/master/LICENSE |
 | SeqSero2 | GNU GPLv2 | https://github.com/denglab/SeqSero2/blob/master/LICENSE |