From 1d97040d0a6ccb708738367e66eb3f42621602de Mon Sep 17 00:00:00 2001 From: Rixing Xu Date: Fri, 14 Jul 2023 14:37:26 -0700 Subject: [PATCH 1/7] add nextflow_schema json --- nextflow_schema.json | 60 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 nextflow_schema.json diff --git a/nextflow_schema.json b/nextflow_schema.json new file mode 100644 index 0000000..972c8e8 --- /dev/null +++ b/nextflow_schema.json @@ -0,0 +1,60 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/nf-artist/dsl2/nextflow_schema.json", + "title": "Sage-Bionetworks-Workflows/nf-artist parameters", + "description": "Nextflow pipeline for GENIE BPC processing", + "type": "object", + "definitions": { + "parameters": { + "title": "Input options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define HTAN Artist pipeline parameters.", + "properties": { + "input": { + "type": "string", + "description": "Path to a file with a file path, uid, or synapseID per row" + }, + "outdir": { + "type": "string", + "description": "Description for this cohort run of the BPC pipeline", + "default": "NSCLC public release update" + }, + "remove_bg": { + "type": "boolean", + "description": "Whether to Keep the background in thumbnails", + "default": true, + "enum": [ + true, + false + ] + }, + "level": { + "type": "integer", + "description": "the pyramid level used in thumbnauls, Default: -1 (highest)", + "default": -1 + }, + "dimred": { + "type": "string", + "description": "", + "default": "umap" + }, + "colormap": { + "type": "boolean", + "description": "", + "default": "UCIE" + }, + "n_components": { + "type": "integer", + "description": "", + "default": 3 + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/parameters" + } + ] +} \ No newline at end of file From 5c0ab947983ed186da4ec59962c1a93248a5bfe9 Mon Sep 17 00:00:00 2001 From: Rixing Xu Date: Fri, 14 Jul 2023 14:42:00 -0700 Subject: [PATCH 2/7] add specs about input filepath --- nextflow_schema.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 972c8e8..287632e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -13,6 +13,8 @@ "properties": { "input": { "type": "string", + "format": "file-path", + "mimetype": "text/csv", "description": "Path to a file with a file path, uid, or synapseID per row" }, "outdir": { From cc4bc6d4a75faad2349b19d728c45f46307e51a2 Mon Sep 17 00:00:00 2001 From: Rixing Xu Date: Fri, 14 Jul 2023 14:43:14 -0700 Subject: [PATCH 3/7] correct colormap type --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 287632e..74a7939 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -42,7 +42,7 @@ "default": "umap" }, "colormap": { - "type": "boolean", + "type": "string", "description": "", "default": "UCIE" }, From f7d57ab2af85c4c40df64a652622d3f101b9b9b0 Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Thu, 17 Aug 2023 16:34:23 +0100 Subject: [PATCH 4/7] Update schema --- nextflow_schema.json | 37 ++++--------------------------------- 1 file changed, 4 insertions(+), 33 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 74a7939..e5a1d3a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/nf-artist/dsl2/nextflow_schema.json", "title": "Sage-Bionetworks-Workflows/nf-artist parameters", - "description": "Nextflow pipeline for GENIE BPC processing", + "description": "Nextflow pipeline for generating Minerva stories and Miniature thumbnails from multiplexed tissue imaging datasets", "type": "object", "definitions": { "parameters": { @@ -15,41 +15,12 @@ "type": "string", "format": "file-path", "mimetype": "text/csv", - "description": "Path to a file with a file path, uid, or synapseID per row" + "description": "Path to a CSV samplesheet" }, "outdir": { "type": "string", - "description": "Description for this cohort run of the BPC pipeline", - "default": "NSCLC public release update" - }, - "remove_bg": { - "type": "boolean", - "description": "Whether to Keep the background in thumbnails", - "default": true, - "enum": [ - true, - false - ] - }, - "level": { - "type": "integer", - "description": "the pyramid level used in thumbnauls, Default: -1 (highest)", - "default": -1 - }, - "dimred": { - "type": "string", - "description": "", - "default": "umap" - }, - "colormap": { - "type": "string", - "description": "", - "default": "UCIE" - }, - "n_components": { - "type": "integer", - "description": "", - "default": 3 + "description": "Directory in which outputs are placed", + "default": "outputs" } } } From cad392082d5bbeea7cc5c10e54653eb96c838907 Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Fri, 18 Aug 2023 10:51:20 +0100 Subject: [PATCH 5/7] Update schema --- nextflow_schema.json | 47 +++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 44 insertions(+), 3 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index e5a1d3a..a3b8c5b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -5,11 +5,12 @@ "description": "Nextflow pipeline for generating Minerva stories and Miniature thumbnails from multiplexed tissue imaging datasets", "type": "object", "definitions": { - "parameters": { - "title": "Input options", + "input_output_options": { + "title": "Input/output options", "type": "object", "fa_icon": "fas fa-terminal", - "description": "Define HTAN Artist pipeline parameters.", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["input", "outdir"], "properties": { "input": { "type": "string", @@ -23,6 +24,46 @@ "default": "outputs" } } + }, + "miniatue_options": { + "title": "Miniature options", + "type": "object", + "fa_icon": "fas fa-palette", + "description": "Define HTAN Artist pipeline parameters.", + "properties": { + "remove_bg": { + "type": "boolean", + "description": "Whether to Keep the background in thumbnails", + "default": true, + "enum": [ + true, + false + ] + }, + "level": { + "type": "integer", + "description": "The pyramid level used in thumbnauls, Default: -1 (smallest)", + "default": -1 + }, + "dimred": { + "type": "string", + "description": "The dimensionality reduction method used", + "default": "umap", + "enum": ["umap", "tsne", "pca"] + }, + "colormap": { + "type": "string", + "description": "The colormap used. Ensure colormap is compatiable with `n_components` selected ", + "enum": ["UCIE", "LAB", "RGB", "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER","CUBEDIAGONAL"], + "default": "UCIE" + }, + "n_components": { + "type": "integer", + "description": "", + "default": 3, + "enum": [2,3] + } + } } }, "allOf": [ From 494ff04028e60586c8c98078882efcbf2f0eed5a Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Fri, 18 Aug 2023 10:52:27 +0100 Subject: [PATCH 6/7] Update schema --- nextflow_schema.json | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index a3b8c5b..034f74c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -34,11 +34,7 @@ "remove_bg": { "type": "boolean", "description": "Whether to Keep the background in thumbnails", - "default": true, - "enum": [ - true, - false - ] + "default": true }, "level": { "type": "integer", From ab171da8121e5360844d249e2442b6ecac5c51d1 Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Fri, 18 Aug 2023 10:59:13 +0100 Subject: [PATCH 7/7] Refine remove_bg description --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 034f74c..641dfe9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -33,7 +33,7 @@ "properties": { "remove_bg": { "type": "boolean", - "description": "Whether to Keep the background in thumbnails", + "description": "Remove non-tissue background", "default": true }, "level": {