updated snapshots for JDK 17

LANL-Bioinformatics · Dec 10, 2024 · 1cd85d7 · 1cd85d7
1 parent eddba05
commit 1cd85d7
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Showing 3 changed files with 3 additions and 6 deletions.
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -20,13 +20,12 @@ jobs:
         uses: eWaterCycle/setup-apptainer@v2
         with:
           apptainer-version: 1.3.0
-      - name: Run an apptainer container
-        run: apptainer run docker://alpine cat /etc/os-release
+
 
       - name: Setup Nextflow latest-edge
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "latest-edge"
+          version: "24.10.1"
 
       - name: Install nf-test
         run: |

diff --git a/modules/hostRemoval/hostRemoval.nf b/modules/hostRemoval/hostRemoval.nf
@@ -172,14 +172,12 @@ workflow HOSTREMOVAL{
         paired = collectCleanPairedReads.out.paired
         //calculate overall stats and create PDF
         hostRemovalStats(settings, hostRemoval.out.cleanstats.collect(), collectCleanPairedReads.out.hostMerged)
-        paired.view()
     } 
     else {
         //no need to merge if only reads from one host were removed
         paired = collectCleanPairedReadsOneHost(settings, cleaned1_ch.concat(cleaned2_ch)).collect()
         //calculate overall stats and create PDF
         hostRemovalStats(settings, hostRemoval.out.cleanstats.collect(), hostRemoval.out.hostReads)
-        paired.view()
     }
     //merge clean unpaired reads (removing any duplicates by read name)
     unpaired = collectCleanSingleReads(settings, hostRemoval.out.cleanedSingleton.collect())

diff --git a/nextflow.config b/nextflow.config
@@ -116,7 +116,7 @@ params {
 }
 
 //container settings
-singularity {
+apptainer {
     enabled = true
     pullTimeout = "1 hour"
     runOptions = "--compat"