From 53c72e7ab7d1da3578d6e58628e5a256095bcbe2 Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Wed, 31 Jan 2024 09:12:33 +0100 Subject: [PATCH] Update output arguments Co-authored-by: Robrecht Cannoodt --- src/featurecounts/config.vsh.yaml | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/src/featurecounts/config.vsh.yaml b/src/featurecounts/config.vsh.yaml index 993266a4..74f3129d 100644 --- a/src/featurecounts/config.vsh.yaml +++ b/src/featurecounts/config.vsh.yaml @@ -35,37 +35,35 @@ functionality: - name: Outputs arguments: - - name: --output + - name: --output_counts alternatives: ["-o"] type: file direction: output description: | - Name of output file including read counts. A separate file including summary statistics of counting results is also included in the output ('.summary'). Both files are in tab delimited format. - must_exist: true - example: features.txt + Name of output file including read counts in tab delimited format. + required: true + example: features.tsv - name: --output_summary type: file direction: output description: | - Summary statistics of counting results is also included in the output ('.summary'). - must_exist: true - example: features.txt.summary + Summary statistics of counting results in tab delimited format. + required: false + example: summary.tsv - name: --output_junctions type: file direction: output description: | - Count of number of reads supporting each exon-exon junction. See '--junctions' for more information. - must_exist: false - example: features.txt.jcounts - must_exist: false - - name: --r_path + Count of number of reads supporting each exon-exon junction. This file is only created if `--junctions` is specified. + example: junctions.txt + required: false + - name: --results_path type: file direction: output description: | - Directory to save the detailed assignment results. If unspecified, the directory where counting results are saved is used. See -R for more format information. - must_exist: false + Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results. example: detailed_results/ - must_exist: false + required: false - name: Annotation arguments: