From 733d3dc8c57078a7c2032ef028429aefc552e3de Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 27 Oct 2022 14:19:28 +0200 Subject: [PATCH 1/2] Apply suggestions from code review --- nextflow_schema.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 59131b6..5c60775 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -753,7 +753,10 @@ "properties": { "preprocessing_qc_tool": { "type": "string", - "default": "fastqc" + "default": "fastqc", + "enum": ["fastqc", "falco"], + "help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.", + "description": "Specify the tool used for quality control of raw sequencing reads" } } } From a402ee3be200089757096207dba17cb1b4ffb5a6 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 27 Oct 2022 12:20:08 +0000 Subject: [PATCH 2/2] [automated] Fix linting with Prettier --- nextflow_schema.json | 50 +++++++------------------------------------- 1 file changed, 7 insertions(+), 43 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5c60775..04ba938 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,11 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "input", - "databases", - "outdir" - ], + "required": ["input", "databases", "outdir"], "properties": { "input": { "type": "string", @@ -84,10 +80,7 @@ "shortread_qc_tool": { "type": "string", "default": "fastp", - "enum": [ - "fastp", - "adapterremoval" - ], + "enum": ["fastp", "adapterremoval"], "fa_icon": "fas fa-tools", "description": "Specify which tool to use for short-read QC" }, @@ -146,11 +139,7 @@ "shortread_complexityfilter_tool": { "type": "string", "default": "bbduk", - "enum": [ - "bbduk", - "prinseqplusplus", - "fastp" - ], + "enum": ["bbduk", "prinseqplusplus", "fastp"], "fa_icon": "fas fa-hammer", "description": "Specify which tool to use for complexity filtering" }, @@ -184,10 +173,7 @@ "shortread_complexityfilter_prinseqplusplus_mode": { "type": "string", "default": "entropy", - "enum": [ - "entropy", - "dust" - ], + "enum": ["entropy", "dust"], "fa_icon": "fas fa-check-square", "description": "Specify the complexity filter mode for PRINSEQ++" }, @@ -361,15 +347,7 @@ "diamond_output_format": { "type": "string", "default": "tsv", - "enum": [ - "blast", - "xml", - "txt", - "daa", - "sam", - "tsv", - "paf" - ], + "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"], "fa_icon": "fas fa-file", "description": "Specify output format from DIAMOND profiling.", "help_text": "DIAMOND can produce output in a number of different formats, you can specify here which to produce.\n\nNote that DIAMOND can only produce one format at a time, and depending on which you pick, some downstream steps may not be executed. For example, selecting `daa` or `sam` will mean you will not get a tabular taxonomic profile as with the other tools.\n\nWill be overriden by `--diamond_save_reads.`\n\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`" @@ -388,14 +366,7 @@ "kaiju_taxon_rank": { "type": "string", "default": "species", - "enum": [ - "phylum", - "class", - "order", - "family", - "genus", - "species" - ], + "enum": ["phylum", "class", "order", "family", "genus", "species"], "fa_icon": "fas fa-tag", "description": "Specify taxonomic rank to be displayed in Kaiju taxon table", "help_text": "Specify the taxonomic level(s) to be displayed in the resulting Kaiju taxon table, as generated by the kaiju2table helper tool.\n\nThis can be either a single level (e.g. `species`), or a comma separated list to display the full taxonomic path (e.g. `superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`" @@ -590,14 +561,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email_on_fail": {