From d57e60e38da760c0132fb9490c48521b99a1e041 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Wed, 23 Oct 2024 11:55:01 +0000 Subject: [PATCH 1/5] fix nextflow_schema.json structure --- nextflow_schema.json | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 679f7d04..f136e2fa 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -101,6 +101,10 @@ "description": "Demultiplexer to use.", "fa_icon": "fas fa-microscope", "default": "bclconvert" + }, + "strandedness": { + "type": "string", + "default": "auto" } } }, @@ -282,11 +286,5 @@ { "$ref": "#/$defs/generic_options" } - ], - "properties": { - "strandedness": { - "type": "string", - "default": "auto" - } - } + ] } From 3ccf8ec50c154520f7564a26f36a82b863bb79b8 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 24 Oct 2024 14:40:39 +0000 Subject: [PATCH 2/5] add downstream csv options group --- nextflow_schema.json | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index f136e2fa..a890d605 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -101,10 +101,20 @@ "description": "Demultiplexer to use.", "fa_icon": "fas fa-microscope", "default": "bclconvert" - }, + } + } + }, + "downstream_csv_options": { + "title": "Downstream CSV options", + "type": "object", + "description": "Options to customize downstream csv creation", + "default": "", + "properties": { "strandedness": { "type": "string", - "default": "auto" + "default": "auto", + "description": "Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet. Accepted values are 'unstranded', 'auto', 'forward', or 'reverse'.", + "fa_icon": "fas fa-arrows-alt-v" } } }, @@ -277,6 +287,9 @@ { "$ref": "#/$defs/demultiplex_options" }, + { + "$ref": "#/$defs/downstream_csv_options" + }, { "$ref": "#/$defs/institutional_config_options" }, From 5042a15a903e1839fd1d491e49c79646c3e2616f Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 24 Oct 2024 15:07:02 +0000 Subject: [PATCH 3/5] add enum options --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index a890d605..200dfcbd 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -112,6 +112,7 @@ "properties": { "strandedness": { "type": "string", + "enum": ["unstranded", "auto", "reverse", "forward"], "default": "auto", "description": "Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet. Accepted values are 'unstranded', 'auto', 'forward', or 'reverse'.", "fa_icon": "fas fa-arrows-alt-v" From 6c9d47b3be6d1e463a7232ac87d386bb49655347 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 24 Oct 2024 12:09:51 -0300 Subject: [PATCH 4/5] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 200dfcbd..30308ece 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -114,7 +114,7 @@ "type": "string", "enum": ["unstranded", "auto", "reverse", "forward"], "default": "auto", - "description": "Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet. Accepted values are 'unstranded', 'auto', 'forward', or 'reverse'.", + "description": "Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet, "fa_icon": "fas fa-arrows-alt-v" } } From 320037a22252b65c4d5ae0137b11190d8a8825f8 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 24 Oct 2024 15:11:49 +0000 Subject: [PATCH 5/5] fix comma --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 30308ece..8558c86e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -114,7 +114,7 @@ "type": "string", "enum": ["unstranded", "auto", "reverse", "forward"], "default": "auto", - "description": "Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet, + "description": "Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet", "fa_icon": "fas fa-arrows-alt-v" } }