Removed TXT options from nextflow schema except for proteinGroups.txt

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))

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"