From 1cd85d7c872032b9f3a884bb6a2a73d7b8673799 Mon Sep 17 00:00:00 2001
From: Andre Watson <andre.watson22@gmail.com>
Date: Mon, 9 Dec 2024 18:11:21 -0700
Subject: [PATCH] updated snapshots for JDK 17

---
 .github/workflows/ci-tests.yml     | 5 ++---
 modules/hostRemoval/hostRemoval.nf | 2 --
 nextflow.config                    | 2 +-
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 7eb142d..39b3d88 100644
--- 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
index b627e57..3b3083f 100644
--- 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
index 15f3ae1..956f22c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -116,7 +116,7 @@ params {
 }
 
 //container settings
-singularity {
+apptainer {
     enabled = true
     pullTimeout = "1 hour"
     runOptions = "--compat"