Merge branch 'CW-4704-common-sha' into 'dev'

update common sha to bump fastcat to 0.18.6 [CW-4704] See merge request epi2melabs/workflows/wf-template!222
epi2me-labs · Aug 8, 2024 · 13c4703 · 13c4703
2 parents 5c6b2d6 + 880d80c
commit 13c4703
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Showing 7 changed files with 380 additions and 3 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -85,6 +85,7 @@ docker-run:
                 "xam-case14", "xam-case14-s3",
                 "xam-case14-keep_unaligned", "xam-case14-s3-keep_unaligned",
                 "xam-case15", "xam-case15-s3",
+                "xam-case16", "xam-case16-s3",
               ]
     rules:
         # NOTE As we're overriding the rules block for the included docker-run
@@ -569,3 +570,12 @@ docker-run:
           variables:
               NF_WORKFLOW_OPTS: "--bam ${S3_TEST_DATA}/xam_ingress/case15"
               AFTER_NEXTFLOW_CMD: $TEST_CMD ${S3_TEST_DATA}/xam_ingress/case15/ bam $$PWD/$$CI_PROJECT_NAME
+
+        - if: $MATRIX_NAME == "xam-case16"
+          variables:
+              NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case16"
+              AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case16/ bam $$PWD/$$CI_PROJECT_NAME
+        - if: $MATRIX_NAME == "xam-case16-s3"
+          variables:
+              NF_WORKFLOW_OPTS: "--bam ${S3_TEST_DATA}/xam_ingress/case16"
+              AFTER_NEXTFLOW_CMD: $TEST_CMD ${S3_TEST_DATA}/xam_ingress/case16/ bam $$PWD/$$CI_PROJECT_NAME
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v5.2.3]
+### Changed
+- Updated wf-common image to shad399cf22079b5b153920ac39ee40095a677933f1 to include latest fastcat (v0.18.6).
+
 ## [v5.2.2]
 ### Changed
 - Matching RG.IDs found in XAM headers are now combined across all input XAM for a particular sample and emitted once, instead of emitting new RG.IDs for each XAM file.

diff --git a/nextflow.config b/nextflow.config
@@ -43,7 +43,7 @@ params {
         example_cmd = [
             "--fastq 'wf-template-demo/test_data/reads.fastq.gz'",
         ]
-        common_sha = "shab540ba556d0d8c38bea8fec520f0bdedd9e59520"
+        common_sha = "shad399cf22079b5b153920ac39ee40095a677933f1"
         agent = null
         epi2me_instance = null
         epi2me_user = null
@@ -57,7 +57,7 @@ manifest {
     description     = 'Template workflow'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v5.2.2'
+    version         = 'v5.2.3'
 }
 
 

diff --git a/test_data/xam_ingress/README b/test_data/xam_ingress/README
@@ -111,8 +111,14 @@
     ├── reads1.bam
     └── reads2.bam
 
-# case02 dir1 BAM with additional RG headers with same runid
+# case02 dir1 BAM with additional RG headers with same acquisition style runid
 └── case15
     ├── reads0.bam
     ├── reads1.bam
     └── reads2.bam
+
+# case02 dir1 BAM with additional RG headers with same protocol style runid
+└── case16
+    ├── reads0.bam
+    ├── reads1.bam
+    └── reads2.bam
diff --git a/test_data/xam_ingress/case16/reads0.bam b/test_data/xam_ingress/case16/reads0.bam
diff --git a/test_data/xam_ingress/case16/reads1.bam b/test_data/xam_ingress/case16/reads1.bam
diff --git a/test_data/xam_ingress/case16/reads2.bam b/test_data/xam_ingress/case16/reads2.bam