From e30d3aec983ea837362bd90de8c0ac5f072369c4 Mon Sep 17 00:00:00 2001 From: Sarah Griffiths Date: Fri, 16 Feb 2024 10:23:15 +0000 Subject: [PATCH] DE_analysis params change input types to numeric --- .gitlab-ci.yml | 2 +- CHANGELOG.md | 5 +++++ bin/de_analysis.R | 8 ++++---- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 409ac83..8288b59 100644 --- a/.gitlab-ci.yml +++ b/.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, diff --git a/CHANGELOG.md b/CHANGELOG.md index d77e00f..e8198f4 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/bin/de_analysis.R b/bin/de_analysis.R index d134f20..1927c7a 100755 --- a/bin/de_analysis.R +++ b/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]