From 49cf30a18600009df9862fe18a6c57a565d28f72 Mon Sep 17 00:00:00 2001 From: Nirmayi Date: Thu, 12 Sep 2024 07:58:24 +0200 Subject: [PATCH] change output quant file to an optional argument --- src/salmon/salmon_quant/config.vsh.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/salmon/salmon_quant/config.vsh.yaml b/src/salmon/salmon_quant/config.vsh.yaml index 1f96f0c9..5fa3d48f 100644 --- a/src/salmon/salmon_quant/config.vsh.yaml +++ b/src/salmon/salmon_quant/config.vsh.yaml @@ -24,7 +24,7 @@ argument_groups: description: | Format string describing the library. The library type string consists of three parts: - 1. Relative orientation of the reads: This part is only provided if the library is paired-end, THe possible options are + 1. Relative orientation of the reads: This part is only provided if the library is paired-end, The possible options are I = inward O = outward M = matching @@ -118,7 +118,7 @@ argument_groups: direction: output description: | Salmon quantification file. - required: true + required: false example: quant.sf - name: Basic options @@ -327,7 +327,7 @@ argument_groups: If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead. - name: --mapping_sam type: file - description: Path to file that should output the selective-alignment results in SAM-compatible format. THis option must be provided while using --write_mappings + description: Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings required: false direction: output example: mappings.sam