Cryptogenotyper release v1.5.0

.github/workflows/pr.yaml

@@ -4,7 +4,7 @@ on:
     paths-ignore:
       - '.github/**'
       - 'deprecated/**'
-      - 'docs/**'
+      - 'docs/**'  
       - '*'
   push:
     branches:
@@ -16,6 +16,7 @@ on:
       - 'deprecated/**'
       - 'docs/**'
       - '*'
+
 env:
   GALAXY_FORK: galaxyproject
   GALAXY_BRANCH: release_23.1
@@ -36,7 +37,7 @@ jobs:
   # which are needed in subsequent steps.
   setup:
     name: Setup cache and determine changed repositories
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     outputs:
       galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
       repository-list: ${{ steps.discover.outputs.repository-list }}
@@ -46,7 +47,7 @@ jobs:
       commit-range: ${{ steps.discover.outputs.commit-range }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.10']
     steps:
     - name: Print github context properties
       run: |
@@ -108,11 +109,11 @@ jobs:
     name: Lint tool-list
     needs: setup
     if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.10']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -154,11 +155,11 @@ jobs:
     name: Lint Python scripts
     needs: setup
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.10']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -189,7 +190,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-22.04]
         r-version: ['release']
     steps:
     - uses: actions/checkout@v3
@@ -245,7 +246,7 @@ jobs:
     name: Check file sizes
     needs: setup
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v3
       with:
@@ -274,12 +275,12 @@ jobs:
     name: Test tools
     needs: setup
     if: ${{ needs.setup.outputs.repository-list != '' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.7']
+        python-version: ['3.10']
     services:
       postgres:
         image: postgres:11
@@ -340,10 +341,10 @@ jobs:
     name: Combine chunked test results
     needs: [setup, test]
     if: ${{ always() && needs.setup.outputs.repository-list != '' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.10']
     steps:
     - uses: actions/download-artifact@v4
       with:
@@ -384,10 +385,10 @@ jobs:
     name: Deploy
     needs: [setup, lint, combine_outputs]
     if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'phac-nml' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.10']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -421,7 +422,7 @@ jobs:
     name: Report deploy status
     needs: [deploy]
     if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'phac-nml' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     # report to the PR if deployment failed
     - name: Get PR object
@@ -443,7 +444,7 @@ jobs:
     name: Check workflow success
     needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]
     if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Check tool lint status
       if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }}

tools/cryptogenotyper/.shed.yml

@@ -1,7 +1,7 @@
 categories: [Sequence Analysis]
-description: CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.
+description: CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA (18S) and gp60 markers.
 name: cryptogenotyper
 owner: nml
-long_description: The CryptoGenotyper is a fast and reproducible tool that can be used to classify the genotype of Cryptosporidium samples by directly analyzing the DNA electropherogram files (.ab1) that correspond to two of its characteristic gene markers (SSU rRNA and gp60)
+long_description: The CryptoGenotyper is a fast and reproducible tool that can be used to classify the genotype of Cryptosporidium samples by directly analyzing the DNA electropherogram (.ab1) and FASTA files (.fasta) files that correspond to two of its characteristic gene markers (SSU rRNA and gp60)
 remote_repository_url: https://github.com/phac-nml/CryptoGenotyper
 homepage_url: https://github.com/phac-nml/CryptoGenotyper