Merge pull request #34 from phac-nml/dev

0.4.1 Patch Release

CHANGELOG.md

@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.1] - 2024-12-23
+
+- Updating the version of `GAS` container from 0.1.1 -> [0.1.3](https://github.com/phac-nml/genomic_address_service/pull/18)
+
 ## [0.4.0] - 2024-11-07
 
 - Added the ability to include a `sample_name` column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration.
@@ -52,3 +56,4 @@ Initial release of the Genomic Address Service Clustering pipeline to be used fo
 [0.2.0]: https://github.com/phac-nml/gasclustering/releases/tag/0.2.0
 [0.3.0]: https://github.com/phac-nml/gasclustering/releases/tag/0.3.0
 [0.4.0]: https://github.com/phac-nml/gasclustering/releases/tag/0.4.0
+[0.4.1]: https://github.com/phac-nml/gasclustering/releases/tag/0.4.1

modules/local/gas/mcluster/main.nf

@@ -5,8 +5,8 @@ process GAS_MCLUSTER{
     tag "Denovo Clustering"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genomic_address_service%3A0.1.1--pyh7cba7a3_1' :
-        'biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }"
+        'https://depot.galaxyproject.org/singularity/genomic_address_service%3A0.1.3--pyh7e72e81_0' :
+        'biocontainers/genomic_address_service:0.1.3--pyh7e72e81_0' }"
 
     input:
     path(dist_matrix)

nextflow.config

@@ -229,7 +229,7 @@ manifest {
     description     = """IRIDA Next Genomic Address Service Clustering Pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.4.0'
+    version         = '0.4.1'
     doi             = ''
     defaultBranch   = 'main'
 }

tests/data/clusters/expected_tree-mismatched-ids.nwk

@@ -1 +1 @@
-((sampleB:0.000000,sampleA:0.000000):16.666666666666668,sampleC:33.333333);
+((sampleB:0.000000,sampleA:0.000000):33.333333333333336,sampleC:33.333333);

tests/data/clusters/expected_tree-partial-mismatched-ids.nwk

@@ -1 +1 @@
-((sampleB:0.000000,sampleA:0.000000):16.666666666666668,sample3:33.333333);
+((sampleB:0.000000,sampleA:0.000000):33.333333333333336,sample3:33.333333);

tests/data/clusters/expected_tree.nwk

@@ -1 +1 @@
-((sample2:0.000000,sample1:0.000000):16.666666666666668,sample3:33.333333);
+((sample2:0.000000,sample1:0.000000):33.333333333333336,sample3:33.333333);

tests/data/clusters/expected_tree_hamming.nwk

@@ -1 +1 @@
-((sample2:1.000000,sample1:1.000000):0.75,sample3:2.500000);
+((sample2:1.000000,sample1:1.000000):1.5,sample3:2.500000);

tests/data/clusters/expected_tree_hamming_complete_linkage.nwk

@@ -1 +1 @@
-((sample2:1.000000,sample1:1.000000):1.0,sample3:3.000000);
+((sample2:1.000000,sample1:1.000000):2.0,sample3:3.000000);

tests/data/clusters/expected_tree_hamming_single_linkage.nwk

@@ -1 +1 @@
-((sample2:1.000000,sample1:1.000000):0.5,sample3:2.000000);
+((sample2:1.000000,sample1:1.000000):1.0,sample3:2.000000);

tests/data/clusters/expected_tree_hash_missing.nwk

@@ -1 +1 @@
-((sample2:1.000000,sample1:1.000000):0.25,sample3:1.500000);
+((sample2:1.000000,sample1:1.000000):0.5,sample3:1.500000);