Merge branch 'new-report-container' into 'dev'

Update aplanat

See merge request epi2melabs/workflows/wf-tb-amr!368

.gitlab-ci.yml

@@ -11,6 +11,8 @@ variables:
     NF_WORKFLOW_OPTS: "--fastq test_data/fastq --sample_sheet test_data/sample_sheet.csv"
     NF_IGNORE_PROCESSES: "downSample"
     CI_FLAVOUR: "new"
+    PYTEST_CONTAINER_NAME: "wf-tb-amr-v1"
+    PYTEST_CONTAINER_CONFIG_KEY: "container_sha="
 # pytest:
 #     image: ubuntu:20.04
 #     stage: preflight

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 - Updated documentation
 - Reconciled workflow with wf-template v5.2.6
+- Updated aplanat to v0.6.20
 
 ## [v1.0.15]
 ### Changed

nextflow.config

@@ -52,7 +52,7 @@ params {
             "--sample_sheet 'wf-tb-amr-demo/sample_sheet.csv'"
         ]
         agent = null
-        container_sha = "sha837f62ff13f7f65a6d58f4d0aff6a9f86dda6fb7"
+        container_sha = "sha3fd3e61673ac6fb1f38d780b1678f6c4685124c0"
         common_sha = "shad28e55140f75a68f59bbecc74e880aeab16ab158"
     }
 }
@@ -81,7 +81,7 @@ env {
 
 process {
     withLabel:microbial { 
-        container = "ontresearch/wf-tb-amr:${params.wf.container_sha}" 
+        container = "ontresearch/wf-tb-amr-v1:${params.wf.container_sha}" 
     }
     withLabel:wf_common {
         container = "ontresearch/wf-common:${params.wf.common_sha}"
@@ -120,7 +120,7 @@ profiles {
             queue = "${params.aws_queue}"
             memory = '8G'
             withLabel:microbial {
-                container = "${params.aws_image_prefix}-wf-tb-amr:${params.wf.container_sha}"
+                container = "${params.aws_image_prefix}-wf-tb-amr-v1:${params.wf.container_sha}"
             }
             withLabel:wf_common {
                 container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"