From 1275b9664eea0f1e3d7a06e4fed834251727bfd6 Mon Sep 17 00:00:00 2001 From: Bart Charbon Date: Wed, 4 Dec 2024 09:38:01 +0100 Subject: [PATCH] Replace Illumina with nanopore as default sequencing platform (#656) --- docs/usage/input.md | 2 +- vip_fastq.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage/input.md b/docs/usage/input.md index 5c99474f..0dd220de 100644 --- a/docs/usage/input.md +++ b/docs/usage/input.md @@ -45,7 +45,7 @@ The following sections describe the columns that can be used in every sample-she | ``fastq`` | ``file list`` | yes3 | | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. single-reads file(s) | | ``fastq_r1`` | ``file list`` | yes3 | | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. paired-end reads file(s) #1 | | ``fastq_r2`` | ``file list`` | yes3 | | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. paired-end reads file(s) #2 | -| ``sequencing_platform`` | ``enum`` | | ``illumina`` | allowed values: [``illumina``,``nanopore``,``pacbio_hifi``], value must be the same for all project samples | +| ``sequencing_platform`` | ``enum`` | | ``nanopore`` | allowed values: [``illumina``,``nanopore``,``pacbio_hifi``], value must be the same for all project samples | 3 Either the `fastq` or the ``fastq_r1`` and ``fastq_r2`` are required. diff --git a/vip_fastq.nf b/vip_fastq.nf index 0565686f..334350f4 100644 --- a/vip_fastq.nf +++ b/vip_fastq.nf @@ -106,7 +106,7 @@ def parseSampleSheet(params) { ], sequencing_platform: [ type: "string", - default: { 'illumina' }, + default: { 'nanopore' }, enum: ['illumina', 'nanopore', 'pacbio_hifi'], scope: "project" ]