Merge branch 'tag-v0.4.2' into 'dev'

tag v0.4.2

See merge request epi2melabs/workflows/wf-transcriptomes!140

CHANGELOG.md

@@ -4,8 +4,11 @@ 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]
+## [v0.4.2]
+### Changed
 - Sample sheet must include a `control` type to indicate which samples are the reference for the differential expression pipeline.
+### Removed
+- Default local executor CPU and RAM limits.
 
 ## [v0.4.1]
 ### Changed

bin/workflow_glue/check_sample_sheet.py

@@ -2,6 +2,7 @@
 import codecs
 import csv
 import os
+import re
 import sys
 
 from .util import get_named_logger, wf_parser  # noqa: ABS101
@@ -79,6 +80,19 @@ def main(args):
         sys.stdout.write(f"Parsing error: {e}")
         sys.exit()
 
+    # check barcodes are correct format
+    for barcode in barcodes:
+        if not re.match(r'^barcode\d\d+$', barcode):
+            sys.stdout.write("values in 'barcode' column are incorrect format")
+            sys.exit()
+
+    # check barcodes are all the same length
+    first_length = len(barcodes[0])
+    for barcode in barcodes[1:]:
+        if len(barcode) != first_length:
+            sys.stdout.write("values in 'barcode' column are different lengths")
+            sys.exit()
+
     # check barcode and alias values are unique
     if len(barcodes) > len(set(barcodes)):
         sys.stdout.write("values in 'barcode' column not unique")

nextflow.config

@@ -110,15 +110,9 @@ manifest {
     description     = 'Transcriptome analysis including gene fusions, differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v0.4.1'
+    version         = 'v0.4.2'
 }
 
-executor {
-    $local {
-        cpus = 4
-        memory = "8 GB"
-    }
-}
 
 epi2melabs {
   tags = "isoforms, transcriptomics"