From b2088bcbb3bfc1057543df056783dcb3defdfd4a Mon Sep 17 00:00:00 2001 From: "Moritz E. Beber" Date: Sun, 4 Dec 2022 21:53:38 +0100 Subject: [PATCH] docs: improve description of `shortread_qc_includeunmerged` --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 350830c..02085d5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -128,8 +128,8 @@ "shortread_qc_includeunmerged": { "type": "boolean", "fa_icon": "far fa-times-circle", - "description": "Include unmerged reads from paired-end merging in the downstream processing", - "help_text": "Turns on the inclusion of unmerged reads in resulting processing FASTQ file of paired-end sequencing data when using `fastp`.\n\nExcluding unmerged reads can be useful in cases where you prefer to have very short reads (e.g. aDNA), thus excluding longer-reads or possibly faulty reads where one of the pair was discarded.\n\n> Modifies tool parameter(s):\n> - adds option `--include_unmerged`\n" + "description": "Include unmerged reads from paired-end merging in the downstream analysis", + "help_text": "Turns on the inclusion of unmerged reads in resulting FASTQ file from merging paired-end sequencing data when using `fastp` and/or `AdapterRemoval`. For `fastp` this means the unmerged read pairs are directly included in the output FASTQ file. For `AdapterRemoval`, additional output files containing unmerged reads are all concatenated into one file by the workflow.\n\nExcluding unmerged reads can be useful in cases where you prefer to have very short reads (e.g. aDNA), thus excluding longer-reads or possibly faulty reads where one of the pair was discarded.\n\n> Adds `fastp` option: `--include_unmerged`\n" }, "shortread_qc_minlength": { "type": "integer",