Replace Illumina with nanopore as default sequencing platform (#656)

molgenis · Dec 4, 2024 · 1275b96 · 1275b96
1 parent 1b7535c
commit 1275b96
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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`` | yes<sup>3</sup> |              | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. single-reads file(s)                               |
 | ``fastq_r1``            | ``file list`` | yes<sup>3</sup> |              | allowed file extensions: [``fastq``, ``fastq.gz``, ``fq``, ``fq.gz``]. paired-end reads file(s) #1                        |
 | ``fastq_r2``            | ``file list`` | yes<sup>3</sup> |              | 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               |
 
 <sup>3</sup> Either the `fastq` or the ``fastq_r1`` and ``fastq_r2`` are required.
 

diff --git 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"
     ]