Merge branch 'pychopper_primer_CW_4184' into 'dev'

Add new cDNA kits

See merge request epi2melabs/workflows/wf-transcriptomes!177

CHANGELOG.md

@@ -4,11 +4,13 @@ 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).
 
-## [Unreleased]
+## [1.3.0]
 ### Removed
 - Fusion detection subworkflow, as the functionality is not robust enough for general use at this time.
 ### Changed
-- Updated pychopper to 2.7.10 
+- Updated pychopper to 2.7.10
+## Added 
+- new `cdna_kit` options: PCS114 and PCB111/114
 
 ## [v1.2.1]
 ### Changed

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
     """
 }

nextflow.config

@@ -95,7 +95,7 @@ params {
       ]
     agent = null
     container_sha = "shafb1e2372e1535f0b42891ed2c68ffdac2ca1d658"
-	common_sha = "sha8b5843d549bb210558cbb676fe537a153ce771d6"
+	common_sha = "shab540ba556d0d8c38bea8fec520f0bdedd9e59520"
     }
 }
 
@@ -106,7 +106,7 @@ manifest {
     description     = 'Transcriptome analysis including differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.2.1'
+    version         = 'v1.3.0'
 }
 
 epi2melabs {

nextflow_schema.json

@@ -256,6 +256,9 @@
                         "SQK-PCS109",
                         "SQK-PCS110",
                         "SQK-PCS111",
+                        "SQK-PCS114",
+                        "SQK-PCB111",
+                        "SQK-PCB114",
                         "SQK-LSK114"
                     ],
                     "description": "If cDNA reads are used, select the kit used.",