From 20a6b46e7edf1227669d1d8c298abfe0790b98a1 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 4 Jun 2024 09:09:54 +0200 Subject: [PATCH] Include cellrangerarc in checker --- workflows/scrnaseq.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf index 526b2e9c..5c789c57 100644 --- a/workflows/scrnaseq.nf +++ b/workflows/scrnaseq.nf @@ -28,12 +28,12 @@ workflow SCRNASEQ { main: protocol_config = Utils.getProtocol(workflow, log, params.aligner, params.protocol) - if (protocol_config['protocol'] == 'auto' && params.aligner !in ["cellranger", "cellrangermulti"]) { + if (protocol_config['protocol'] == 'auto' && params.aligner !in ["cellranger", "cellrangerarc", "cellrangermulti"]) { error "Only cellranger supports `protocol = 'auto'`. Please specify the protocol manually!" } ch_genome_fasta = params.fasta ? file(params.fasta, checkIfExists: true) : ( params.genome ? file( getGenomeAttribute('fasta'), checkIfExists: true ) : [] ) - ch_gtf = params.gtf ? file(params.gtf, checkIfExists: true) : ( params.genome ? file( getGenomeAttribute('gtf'), checkIfExists: true ) : [] ) + ch_gtf = params.gtf ? file(params.gtf , checkIfExists: true) : ( params.genome ? file( getGenomeAttribute('gtf') , checkIfExists: true ) : [] ) // general input and params ch_transcript_fasta = params.transcript_fasta ? file(params.transcript_fasta): []