From d37e870fded373745f7d67e0e733406c6d9a6f1e Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 23 Oct 2024 08:53:16 +0200 Subject: [PATCH] Removed TXT options from nextflow schema except for proteinGroups.txt --- CHANGELOG.md | 2 +- nextflow_schema.json | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c5ad741..73234251 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed -- [[#304](https://github.com/nf-core/differentialabundance/pull/304)] - Fix bug when using TXT contrast file ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) +- [[#304](https://github.com/nf-core/differentialabundance/pull/304)] - Removed TXT file options from nextflow_schema where they are equivalent to TSV to make the input files clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#299](https://github.com/nf-core/differentialabundance/pull/299)] - Add exclusions for 3.0.1 template update ([@pinin4fjords](https://github.com/pinin4fjords)) - [[#289](https://github.com/nf-core/differentialabundance/pull/289)] - Fix missing ch_gene_sets default for gprofiler2 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#282](https://github.com/nf-core/differentialabundance/pull/282)] - In order to improve resumability, create a copy of the matrix as an annotation file only if necessary; add original matrix file name to copy name ([@bjlang](https://github.com/bjlang), review by [@WackerO](https://github.com/WackerO)) diff --git a/nextflow_schema.json b/nextflow_schema.json index 7ac1f1ef..47442fd5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -32,7 +32,7 @@ "format": "file-path", "exists": true, "mimetype": "text/csv", - "pattern": "^\\S+\\.(csv|tsv|txt)$", + "pattern": "^\\S+\\.(csv|tsv)$", "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/differentialabundance/usage#samplesheet-input).", @@ -42,7 +42,7 @@ "type": "string", "description": "A CSV file describing sample contrasts", "help_text": "This file is used to define groups of samples from 'input' to compare. It must contain at least the columns 'variable', 'reference', 'target' and 'blocking', where 'variable' is a column in the input sample sheet, 'reference' and 'target' are values in that column, and blocking is a colon-separated list of additional 'blocking' variables (can be an empty string)", - "pattern": "^\\S+\\.(csv|tsv|txt)$", + "pattern": "^\\S+\\.(csv|tsv)$", "format": "file-path", "mimetype": "text/csv", "fa_icon": "fas fa-adjust" @@ -69,11 +69,11 @@ "properties": { "matrix": { "type": "string", - "description": "TSV-format abundance matrix", + "description": "TSV/CSV-format abundance matrix", "help_text": "For example an expression matrix output from the nf-core/rnaseq workflow. There must be a column in this matrix for every row in the input sample sheet.\n\nNot a required input if providing CEL files for affymetrix preprocessing.", "format": "file-path", "mimetype": "text/tab-separated-values", - "pattern": "^\\S+\\.(tsv|csv|txt)$", + "pattern": "^\\S+\\.(tsv|csv)$|\\S*proteinGroups\\.txt$", "fa_icon": "fas fa-border-all" }, "transcript_length_matrix": { @@ -174,7 +174,7 @@ "features": { "type": "string", "mimetype": "text/csv", - "pattern": "^\\S+\\.(csv|tsv|txt)$", + "pattern": "^\\S+\\.(csv|tsv)$", "description": "This parameter allows you to supply your own feature annotations. These can often be automatically derived from the GTF used upstream for RNA-seq, or from the Bioconductor annotation package (for affy arrays). ", "help_text": "This parameter allows you to supply your own feature annotations. These can often be automatically derived from the GTF used upstream for RNA-seq, or from the Bioconductor annotation package (for affy arrays). ", "fa_icon": "fas fa-align-justify"