From c026e8374f3fdd62115a2fbd9f01ad8fe474b6c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=98ens-ftricomi=E2=80=99?= Date: Thu, 15 Aug 2024 16:06:46 +0100 Subject: [PATCH] fix channel name --- pipelines/nextflow/workflows/star_alignment.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipelines/nextflow/workflows/star_alignment.nf b/pipelines/nextflow/workflows/star_alignment.nf index c097c98..e5fa758 100644 --- a/pipelines/nextflow/workflows/star_alignment.nf +++ b/pipelines/nextflow/workflows/star_alignment.nf @@ -91,8 +91,8 @@ workflow STAR_ALIGNMENT { def genomeAndDataToAlign = FETCH_GENOME(data.flatten()) def genomeIndexAndDataToAlign = INDEX_GENOME(genomeAndDataToAlign) - def pairedFastqFiles=DOWNLOAD_PAIRED_FASTQS(runAccessionMetadataRunOutput) - def starOutput = RUN_STAR(genomeIndexAndDataToAlign) + def pairedFastqFiles=DOWNLOAD_PAIRED_FASTQS(genomeIndexAndDataToAlign) + def starOutput = RUN_STAR(pairedFastqFiles) def indexBamOutput = INDEX_BAM (starOutput) if (params.bam2cram){ def cramFile = CONVERT_BAM_TO_CRAM (indexBamOutput)