diff --git a/CHANGELOG.md b/CHANGELOG.md index bd03efe..1cf9837 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/bin/workflow_glue/check_sample_sheet.py b/bin/workflow_glue/check_sample_sheet.py index d77f1ab..fe4fc37 100755 --- a/bin/workflow_glue/check_sample_sheet.py +++ b/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") diff --git a/nextflow.config b/nextflow.config index 9b5ae49..a039050 100644 --- a/nextflow.config +++ b/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"