Merge pull request #17 from peterk87/clair3-biocontainers

Use Clair3 Biocontainers images instead of DockerHub images

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,15 @@
+name: '✨ Feature request'
+description: Suggest a new feature or enhancement for nf-flu
+labels: [enhancement]
+
+body:
+  - id: description
+    type: textarea
+    attributes:
+      label: Problem description
+      description: >
+        Please describe the feature or behavior you'd like to see in nf-flu and the motivation.
+      placeholder: >
+        I wish nf-flu could ...
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/question.yml

@@ -0,0 +1,42 @@
+name: '❓ Question'
+description: Ask a question about nf-flu
+labels: [question]
+
+body:
+  - type: markdown
+    attributes:
+      value: >
+        Have you searched the documentation for nf-flu?
+        Please see the following documentation:
+
+        * [nf-flu Usage](https://github.com/CFIA-NCFAD/nf-flu/blob/master/docs/usage.md)
+        
+        * [nf-flu Output](https://github.com/CFIA-NCFAD/nf-flu/blob/master/docs/output.md)
+        
+        * [nf-flu Quickstart guide](https://github.com/CFIA-NCFAD/nf-flu/blob/master/README.md#quick-start)
+
+        Has your question already been answered?
+        Check here:
+
+        * [previously asked questions](https://github.com/CFIA-NCFAD/nf-flu/issues?q=is%3Aissue+label%3Aquestion)
+        
+        * [bug reports](https://github.com/CFIA-NCFAD/nf-flu/issues?q=is%3Aissue+label%3Abug)
+  - type: checkboxes
+    attributes:
+      label: Research
+      options:
+        - label: >
+            I have searched the documentation and previously asked questions.
+          required: true
+  - type: markdown
+    attributes:
+      value: ---
+  - type: textarea
+    id: question
+    attributes:
+      label: Question about nf-flu
+      description: >
+        Please provide a detailed description of your question.
+        Include any relevant code or command line output.
+      placeholder: |
+        Can nf-flu do X?

.github/workflows/ci.yml

@@ -15,15 +15,15 @@ jobs:
   test_illumina:
     name: Run Illumina test
     # Only run on push if this is the nf-flu dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'peterk87/nf-flu') }}
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CFIA-NCFAD/nf-flu') }}
     runs-on: ubuntu-latest
     env:
       NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.10.6', '22.04.0']
+        nxf_ver: ['21.10.6', '23.04.1']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -86,15 +86,15 @@ jobs:
   test_nanopore:
     name: Run Nanopore test
     # Only run on push if this is the nf-flu dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'peterk87/nf-flu') }}
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CFIA-NCFAD/nf-flu') }}
     runs-on: ubuntu-latest
     env:
       NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.10.6', '22.04.0']
+        nxf_ver: ['21.10.6', '23.04.1']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.1.6](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.1.6)] - 2023-05-31
+
+This is a patch release for a minor change to use Biocontainers Docker and Singularity images for Clair3 to avoid hitting limits on pulls from Docker Hub and since Biocontainers images are half the size of [hkubal/clair3](https://hub.docker.com/r/hkubal/clair3/) images.
+
+Also, updated CI workflow and added issue template forms for feature request and questions.
+
 ## [[3.1.5](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.1.5)] - 2023-05-30
 
 ### Added

modules/local/clair3.nf

@@ -7,9 +7,9 @@ process CLAIR3 {
 
   conda (params.enable_conda ? 'bioconda::clair3==1.0.2' : null)
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'hkubal/clair3:v1.0.2'
+    container 'https://depot.galaxyproject.org/singularity/clair3:1.0.2--py39hb9dc472_0'
   } else {
-    container 'hkubal/clair3:v1.0.2'
+    container 'quay.io/biocontainers/clair3:1.0.2--py39hb9dc472_0'
   }
 
   input:
@@ -38,7 +38,7 @@ process CLAIR3 {
       if [[ ${params.enable_conda} = true ]] ; then
           MODEL_PATH="\$CLAIR_BIN_DIR/${model_suffix}"
       else [[ ${params.enable_conda} = false ]]
-          MODEL_PATH="/opt/models/${params.clair3_variant_model}"
+          MODEL_PATH="/usr/local/bin/models/${params.clair3_variant_model}"
       fi
   fi
 

nextflow.config

@@ -125,7 +125,7 @@ manifest {
   description     = 'Influenza A virus genome assembly pipeline'
   homePage        = 'https://github.com/CFIA-NCFAD/nf-flu'
   author          = 'Peter Kruczkiewicz, Hai Nguyen'
-  version         = '3.1.5'
+  version         = '3.1.6'
   nextflowVersion = '>=21.10'
   mainScript      = 'main.nf'
 }