Version 2.3.2

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
         # Nextflow versions
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: "23.04.4"
+          - NXF_VER: "23.10.1"
     steps:
       - name: Free Disk Space (Ubuntu)
         uses: jlumbroso/free-disk-space@main
@@ -52,6 +52,10 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
+      - name: Mount home dir
+        run: |
+          export NXF_DOCKER_HOME_MOUNT=true
+
       - name: Run ani track test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_ani,docker --out_dir ./results

CHANGELOG.md

@@ -1,6 +1,11 @@
 
 # Changelog
 
+## Version 2.3.2
+- Corrected an issue with the input to ParSNP, as of issue #117
+- Updated the version of Gubbins to 3.3.4
+- Added home mount to the CI test pipeline due to updates with nextflow
+
 ## Version 2.3.1
 - Updated the version of ParSNP to 2.0.3, as of issue #112
 - Updated Panaroo to version 1.3.4

bin/core_genome_report.Rmd

@@ -225,7 +225,7 @@ tool_data <- data.frame(
            "Snp-sites",
            "IQTree"),
   Version = c("2.0.3",
-              "3.3.2",
+              "3.3.4",
               "0.5--1",
               "0.8.2",
               "2.5.1",

bin/mapping_report.Rmd

@@ -196,8 +196,8 @@ tool_data <- data.frame(
            "Snp-sites",
            "IQTree"),
   Version = c("4.6.0",
-              "3.3.2",
-              "0.5",
+              "3.3.4",
+              "0.5--1",
               "0.8.2",
               "2.5.1",
               "2.2.6")

conf/base.config

@@ -11,6 +11,7 @@
 report {
 	enabled		= true
 	file		= "${params.out_dir}/logs/nextflow_run_report.html"
+	overwrite	= true
 }
 
 process {

modules/GUBBINS.nf

@@ -1,6 +1,6 @@
 process GUBBINS {
-	conda (params.enable_conda ? 'bioconda::gubbins=3.2.0' : null)
-	container 'evezeyl/gubbins:3.3.2'
+	conda (params.enable_conda ? 'bioconda::gubbins=3.3.4' : null)
+	container 'quay.io/biocontainers/gubbins:3.3.4--py310pl5321he4a0461_0'
 
 	label 'process_high_memory_time'
 

modules/PARSNP.nf

@@ -5,7 +5,7 @@ process PARSNP {
 	label 'process_long'
 
         input:
-        file("*")
+        file(fasta)
 
         output:
 	path "parsnp_alignment.fasta", emit: fasta_alignment_ch
@@ -15,7 +15,7 @@ process PARSNP {
         script:
         """
 	parsnp --version > parsnp.version
-        parsnp -d *.fasta -p $task.cpus --skip-phylogeny -u -o results -r $params.parsnp_ref -v -c &> parsnp.log
+        parsnp -d $fasta -p $task.cpus --skip-phylogeny -u -o results -r $params.parsnp_ref -v -c &> parsnp.log
 	mv results/log/parsnpAligner.log .
 	mv results/parsnp.ggr .
 	mv results/parsnp.xmfa .

nextflow.config

@@ -157,8 +157,8 @@ manifest {
     homePage        = 'https://github.com/NorwegianVeterinaryInstitute/ALPPACA'
     description     = 'A Tool for Prokaryotic Phylogeny and Clustering Analysis'
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.4'
-    version         = '2.3.1'
+    nextflowVersion = '!>=23.10.1'
+    version         = '2.3.2'
 }
 
 // Define variables to prevent local R libraries from conflicting with the container