From 920c93f9b6b0fd0b84e7d311225dcb2f9dbcf3b6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 18 Feb 2025 10:23:16 +0000 Subject: [PATCH 1/3] Update nextflow_schema.json to demo type issue --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 65d31c68..7aeda3ff 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,6 +15,7 @@ "type": "string", "format": "file-path", "mimetype": "text/tsv", + "pattern": "^\\S+\\.tsv$", "fa_icon": "fas fa-dna", "description": "Path to tab-separated sample sheet", "help_text": "Path to sample sheet, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml), that points to compressed fastq files.\n\nThe sample sheet must have two to four tab-separated columns/entries with the following headers: \n- `sampleID` (required): Unique sample IDs, must start with a letter, and can only contain letters, numbers or underscores\n- `forwardReads` (required): Paths to (forward) reads zipped FastQ files\n- `reverseReads` (optional): Paths to reverse reads zipped FastQ files, required if the data is paired-end\n- `run` (optional): If the data was produced by multiple sequencing runs, any string\n\nRelated parameters are:\n- `--pacbio` and `--iontorrent` if the sequencing data is PacBio data or IonTorrent data (default expected: paired-end Illumina data)\n- `--single_end` if the sequencing data is single-ended Illumina data (default expected: paired-end Illumina data)\n- Choose an appropriate reference taxonomy for the type of amplicon (16S/18S/ITS/CO1) (default: DADA2 assignTaxonomy and 16S rRNA sequence database)", From f811b88f9af1857cbb0a75fb1e55eb0866ff54e7 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 18 Feb 2025 10:35:19 +0000 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8b8d0d21..6032e179 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#800](https://github.com/nf-core/ampliseq/pull/800) - Fixed SH files for UNITE9.0, they were missing some entries due to a bug caused by API update in PlutoF - [#808](https://github.com/nf-core/ampliseq/pull/808) - Add missing library declaration in R script. +- [#832](https://github.com/nf-core/ampliseq/pull/832) - Add pattern to input field ### `Dependencies` From d121b0dc8e96cf0720cc48fb82b97bd9444d66ab Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Wed, 19 Feb 2025 10:44:43 +0100 Subject: [PATCH 3/3] Update nextflow_schema.json --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 7aeda3ff..1075758e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,7 +15,7 @@ "type": "string", "format": "file-path", "mimetype": "text/tsv", - "pattern": "^\\S+\\.tsv$", + "pattern": "^\\S+\\.(tsv|csv|yml|yaml|txt)$", "fa_icon": "fas fa-dna", "description": "Path to tab-separated sample sheet", "help_text": "Path to sample sheet, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml), that points to compressed fastq files.\n\nThe sample sheet must have two to four tab-separated columns/entries with the following headers: \n- `sampleID` (required): Unique sample IDs, must start with a letter, and can only contain letters, numbers or underscores\n- `forwardReads` (required): Paths to (forward) reads zipped FastQ files\n- `reverseReads` (optional): Paths to reverse reads zipped FastQ files, required if the data is paired-end\n- `run` (optional): If the data was produced by multiple sequencing runs, any string\n\nRelated parameters are:\n- `--pacbio` and `--iontorrent` if the sequencing data is PacBio data or IonTorrent data (default expected: paired-end Illumina data)\n- `--single_end` if the sequencing data is single-ended Illumina data (default expected: paired-end Illumina data)\n- Choose an appropriate reference taxonomy for the type of amplicon (16S/18S/ITS/CO1) (default: DADA2 assignTaxonomy and 16S rRNA sequence database)",