Merge branch 'CW-3464' into 'dev'

DE_analysis params change input types to numeric

See merge request epi2melabs/workflows/wf-transcriptomes!161

.gitlab-ci.yml

@@ -175,7 +175,7 @@ docker-run:
                 --ref_genome differential_expression_mouse/GRCm39.genome.fa.gz \
                 --ref_annotation differential_expression_mouse/gencode.vM33.annotation.gtf \
                 --direct_rna --ref_transcriptome differential_expression_mouse/gencode.vM33.transcripts.fa.gz \
-                --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv \
+                --transcriptome_assembly false --sample_sheet differential_expression_mouse/sample_sheet.csv \
                 -c demo.nextflow.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,

CHANGELOG.md

@@ -4,6 +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]
+### Fixed
+- Differential expression failing with 10 or more samples.
+- Regression causing the DE analysis numeric parameters to not be evaluated correctly.
+
 ## [v1.1.0]
 ### Changed
 - Improve documentation around filtering of transcripts done before DTU analysis.

bin/de_analysis.R

@@ -5,10 +5,10 @@ suppressMessages(library("GenomicFeatures"))
 suppressMessages(library("edgeR"))
 args <- commandArgs(trailingOnly=TRUE)
 ref_annotation <- args[1]
-min_samps_gene_expr <- args[2]
-min_samps_feature_expr <- args[3]
-min_gene_expr <- args[4] 
-min_feature_expr <- args[5]
+min_samps_gene_expr <- as.numeric(args[2])
+min_samps_feature_expr <- as.numeric(args[3])
+min_gene_expr <- as.numeric(args[4]) 
+min_feature_expr <- as.numeric(args[5])
 annotation_type <- args[6]
 strip_version <- args[7]