Merge remote-tracking branch 'origin/harmon_fix_gh_actions_test' into…

… single-read-raw-clean
naobservatory · Dec 3, 2024 · e85dd45 · e85dd45
2 parents ad640c6 + 222946d
commit e85dd45
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/.github/workflows/end-to-end.yml b/.github/workflows/end-to-end.yml
@@ -16,10 +16,10 @@ jobs:
           java-version: '11'
           distribution: 'adopt'
 
-      - name: Setup Nextflow latest-edge
+      - name: Setup Nextflow latest (stable)
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "latest-edge"
+          version: "latest"
 
       - name: Install nf-test
         run: |

diff --git a/workflows/run.nf b/workflows/run.nf
@@ -87,9 +87,9 @@ workflow RUN {
     time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt")
     version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt")
     index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json")
-    .map { file -> file.copyTo("${workDir}/params-index.json") }
+    .map { file -> file.copyTo("${params.base_dir}/work/params-index.json") }
     index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt")
-    .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") }
+    .map { file -> file.copyTo("${params.base_dir}/work/pipeline-version-index.txt") }
     publish:
         // Saved inputs
         index_params_ch >> "input"

diff --git a/workflows/run_validation.nf b/workflows/run_validation.nf
@@ -43,9 +43,9 @@ workflow RUN_VALIDATION {
     time_ch = Channel.of(start_time_str + "\n").collectFile(name: "time.txt")
     version_ch = Channel.fromPath("${projectDir}/pipeline-version.txt")
     index_params_ch = Channel.fromPath("${params.ref_dir}/input/index-params.json")
-    .map { file -> file.copyTo("${workDir}/params-index.json") }
+    .map { file -> file.copyTo("${params.base_dir}/work/params-index.json") }
     index_pipeline_version_ch = Channel.fromPath("${params.ref_dir}/logging/pipeline-version.txt")
-    .map { file -> file.copyTo("${workDir}/pipeline-version-index.txt") }
+    .map { file -> file.copyTo("${params.base_dir}/work/pipeline-version-index.txt") }
     publish:
         // Saved inputs
         index_params_ch >> "input"