Merge branch 'template-updates' into 'dev'

template updates See merge request epi2melabs/workflows/wf-amplicon!92
epi2me-labs · Aug 23, 2024 · a7c770a · a7c770a
2 parents 4ed66f0 + deb697c
commit a7c770a
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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).
 
+## [v1.1.3]
+### Fixed
+- Automated basecaller detection failing in some circumstances.
+
 ## [v1.1.2]
 ### Fixed
 - The workflow failing in _de novo_ mode when all reads for a sample came from the same strand.

diff --git a/lib/ingress.nf b/lib/ingress.nf
@@ -621,6 +621,8 @@ process validateIndex {
 }
 
 
+// Sort FOFN for samtools merge to ensure samtools sort breaks ties deterministically.
+// Uses -c to ensure matching RG.IDs across multiple inputs are not unnecessarily modified to avoid collisions.
 process mergeBams {
     label "ingress"
     label "wf_common"
@@ -632,11 +634,12 @@ process mergeBams {
     def merge_threads = Math.max(1, task.cpus - 1)
     """
     samtools merge -@ ${merge_threads} \
-        -b <(find input_bams -name 'reads*.bam') --write-index -o reads.bam##idx##reads.bam.bai
+        -c -b <(find input_bams -name 'reads*.bam' | sort) --write-index -o reads.bam##idx##reads.bam.bai
     """
 }
 
 
+// Sort FOFN for samtools cat to ensure samtools sort breaks ties deterministically.
 process catSortBams {
     label "ingress"
     label "wf_common"
@@ -647,7 +650,7 @@ process catSortBams {
     script:
     def sort_threads = Math.max(1, task.cpus - 2)
     """
-    samtools cat -b <(find input_bams -name 'reads*.bam') \
+    samtools cat -b <(find input_bams -name 'reads*.bam' | sort) \
     | samtools sort - -@ ${sort_threads} --write-index -o reads.bam##idx##reads.bam.bai
     """
 }

diff --git a/nextflow.config b/nextflow.config
@@ -62,7 +62,7 @@ params {
             "--fastq 'wf-amplicon-demo/fastq'",
             "--reference 'wf-amplicon-demo/reference.fa'"
         ]
-        common_sha = "sha8b5843d549bb210558cbb676fe537a153ce771d6"
+        common_sha = "shad399cf22079b5b153920ac39ee40095a677933f1"
         container_sha = "sha79b5ac4013195fec9809f2b71ef55b87bf9c7f16"
         container_sha_medaka = "sha3486abaab0d3b90351617eb8622acf2028edb154"
         agent = null
@@ -76,7 +76,7 @@ manifest {
     description     = 'Amplicon workflow'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.1.2'
+    version         = 'v1.1.3'
 }
 
 epi2melabs {