Merge pull request #106 from umccr/cleanup

Update GitHub Actions

.Rbuildignore

@@ -31,3 +31,4 @@ CODE_OF_CONDUCT.md
 inst/rmd/umccr_portal/html
 inst/rmd/umccr_workflows/umccrise/html
 inst/rmd/umccr_workflows/bcl_convert/html
+inst/rmd/umccr_workflows/alignment_qc/html

.github/workflows/conda_deploy.yaml

@@ -24,26 +24,23 @@ jobs:
 
     steps:
       - name: Code checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Micromamba setup
         uses: mamba-org/setup-micromamba@v1
         with:
-          micromamba-version: '1.4.9-0'
           environment-file: ${{ env.env_yaml_path }}/condabuild.yaml
       - name: 🐍 Conda pkg build and upload
         run: |
           dvc pull
           ls -l inst/extdata/*
-          conda mambabuild --R 4.2 ${recipe_path} --token ${atoken}
+          conda mambabuild --R 4.2 ${recipe_path} -c conda-forge --token ${atoken}
       - name: 🔒 Conda lock
         run: |
-          conda-lock --file ${env_yaml_path}/dracarys.yaml --platform linux-64
-          mv conda-lock.yml ${env_lock_path}/conda-lock.yml
+          conda-lock lock --file ${env_yaml_path}/dracarys.yaml -p linux-64
+          conda-lock render --kind explicit -p linux-64 conda-lock.yml --filename-template 'dracarys-{platform}.lock' && rm conda-lock.yml
+          mv dracarys-*.lock ${env_lock_path}/
       - name: 💾 Commit lockfile
         run: |
-          # TODO: the version bumping guarantees there will be changes,
-          # but during testing this can be problematic - need to
-          # commit only if changes exist.
           git status
           git config --local user.email "actions@github.com"
           git config --local user.name "GitHub Actions"
@@ -67,7 +64,7 @@ jobs:
           LATEST_COMMIT_HASH="$(git --no-pager log -1 --format='%H')"
           echo "latest_commit_hash=${LATEST_COMMIT_HASH}" >> $GITHUB_OUTPUT
       - name: 🔖 Create tag
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         env:
           LATEST_COMMIT_HASH: ${{ steps.pull_lock_commit.outputs.latest_commit_hash }}
         with:
@@ -83,26 +80,26 @@ jobs:
 
       # work with tag from above
       - name: Code checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: v${{ env.VERSION }}
       - name: 🏰 QEMU setup
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       - name: 🏯 Buildx setup
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
         with:
           install: true
           config-inline: |
             [worker.oci]
               max-parallelism = 2
       - name: 🐙 GitHub CR login
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: 🐳 Docker img build and push
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           tags: ghcr.io/${{ github.repository }}:${{ env.VERSION }}
           context: . # yes, dot

Dockerfile

@@ -8,14 +8,14 @@ RUN mamba config \
     mamba install \
       -c conda-forge \
       -c nodefaults \
-      conda-lock==1.3.0 && \
+      conda-lock && \
     mamba clean --all --force-pkgs-dirs
 
+ARG DRACARYS_LOCK="dracarys-linux-64.lock"
 ARG ENV_NAME="dracarys_env"
-COPY ./conda/env/lock/conda-lock.yml .
-RUN conda-lock install --name ${ENV_NAME} conda-lock.yml && \
-    mamba clean --all --force-pkgs-dirs && \
-    rm conda-lock.yml
+COPY ./conda/env/lock/${DRACARYS_LOCK} .
+RUN conda-lock install --name ${ENV_NAME} --file ${DRACARYS_LOCK} && \
+    mamba clean --all --force-pkgs-dirs
 
 ARG MAMBA_PREFIX="/opt/conda"
 ENV PATH="${MAMBA_PREFIX}/envs/${ENV_NAME}/bin:${PATH}"

NAMESPACE

@@ -79,7 +79,6 @@ export(s3_files_list_filter_relevant)
 export(s3_search)
 export(session_info_kable)
 export(time_metrics_process)
-export(tso_rmd)
 export(umccr_tidy)
 importFrom(R6,R6Class)
 importFrom(ggplot2,ggplot)

R/multiqc.R

@@ -373,6 +373,10 @@ multiqc_parse_xyline_plot <- function(dat) {
   if (dat[["config"]][["id"]] %in% c("dragen_coverage_per_contig", "dragen_coverage_per_non_main_contig")) {
     return(multiqc_parse_xyline_plot_contig_cvg(dat))
   }
+  # some empty fastqc_adapter_content_plot - see https://github.com/umccr/dracarys/issues/104
+  if (length(dat[["datasets"]][[1]]) == 0) {
+    return(NULL)
+  }
   dat[["datasets"]][[1]] |>
     purrr::map(
       function(nm_data) {

tests/testthat/test-roxytest-testexamples-dragen.R

@@ -2,7 +2,7 @@
 
 # File R/dragen.R: @testexamples
 
-test_that("Function time_metrics_process() @ L771", {
+test_that("Function time_metrics_process() @ L789", {
 
   p <- system.file("extdata/wgs/SEQC-II.time_metrics.csv.gz", package = "dracarys")
   x <- TimeMetricsFile$new(p)