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Merge pull request #26 from N-Hoffmann/stringtie
Help message and bug fixes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,8 @@ | ||
| // General | ||
| plugins { | ||
| id '[email protected]' | ||
| } | ||
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| params { | ||
| outdir = "results" | ||
| withGeneCoverage = false | ||
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@@ -14,6 +18,7 @@ params { | |
| tfkmers_tokenizer = null | ||
| bambu_strand = true | ||
| tx_discovery = "bambu" | ||
| help = false | ||
| } | ||
|
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||
| process { | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/IGDRion/ANNEXA/master/nextflow_schema.json", | ||
| "title": "IGDRion/ANNEXA pipeline parameters", | ||
| "description": "An all-in-one pipeline to analyze LR-RNAseq data,reconstruct and quantify known and novel genes and isoforms.", | ||
| "type": "object", | ||
| "defs": { | ||
| "required": { | ||
| "title": "Required options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-terminal", | ||
| "description": "Define where the pipeline should find input data and save output data.", | ||
| "properties": { | ||
| "input": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "pattern": "^\\S+\\.(csv|tsv|yaml|json)$", | ||
| "description": "Path to file listing paths to bam files.", | ||
| "fa_icon": "fas fa-file-csv" | ||
| }, | ||
| "fa": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "description": "Path to reference genome.", | ||
| "fa_icon": "fas fa-folder-open" | ||
| }, | ||
| "gtf": { | ||
| "type": "string", | ||
| "format": "directory-path", | ||
| "description": "Path to reference annotation.", | ||
| "fa_icon": "fas fa-folder-open" | ||
| } | ||
| } | ||
| }, | ||
| "profile_options": { | ||
| "title": "Profile options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-terminal", | ||
| "description": "Define how the pipeline should be executed.", | ||
| "properties": { | ||
| "profile test": { | ||
| "type": "string", | ||
| "description": "Run annexa on toy dataset.", | ||
| "fa_icon": "fas fa-file-csv" | ||
| }, | ||
| "profile slurm": { | ||
| "type": "string", | ||
| "description": "Run annexa on slurm executor." | ||
| }, | ||
| "profile singularity": { | ||
| "type": "string", | ||
| "description": "Run annexa in singularity container." | ||
| }, | ||
| "profile conda": { | ||
| "type": "string", | ||
| "description": "Run annexa in conda environment." | ||
| }, | ||
| "profile docker": { | ||
| "type": "string", | ||
| "description": "Run annexa in docker container." | ||
| } | ||
| } | ||
| }, | ||
| "main_options": { | ||
| "title": "Main options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-terminal", | ||
| "description": "General ANNEXA parameters.", | ||
| "properties": { | ||
| "tx_discovery": { | ||
| "type": "string", | ||
| "description": "Specify which transcriptome reconstruction tool to use.", | ||
| "default": "bambu", | ||
| "enum": ["bambu", "stringtie2"], | ||
| "fa_icon": "fas fa-file-csv" | ||
| }, | ||
| "filter": { | ||
| "type": "boolean", | ||
| "description": "Perform or not the filtering step.", | ||
| "default": "true" | ||
| }, | ||
| "withGeneCoverage": { | ||
| "type": "boolean", | ||
| "description": "Run RSeQC (can be long depending on annotation and bam sizes).", | ||
| "default": "false" | ||
| } | ||
| } | ||
| }, | ||
| "bzmbu_options": { | ||
| "title": "Bambu options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-terminal", | ||
| "description": "Parameters related to Bambu.", | ||
| "properties": { | ||
| "bambu_strand": { | ||
| "type": "boolean", | ||
| "description": "Run bambu with stranded data", | ||
| "default": "true" | ||
| }, | ||
| "prefilter_ndr": { | ||
| "type": "boolean", | ||
| "description": "When using ANNEXA with bambu, prefilter before the filtering step. false by default.", | ||
| "default": "false" | ||
| }, | ||
| "bambu_threshold": { | ||
| "type": "integer", | ||
| "description": "bambu NDR threshold below which new transcripts are retained.", | ||
| "default": "0.2" | ||
| } | ||
| } | ||
| }, | ||
| "filtering_options": { | ||
| "title": "Filtering options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-terminal", | ||
| "description": "Parameters related to filtering step.", | ||
| "properties": { | ||
| "tfkmers_tokenizer": { | ||
| "type": "string", | ||
| "description": "Path to TransforKmers tokenizer. Required if filter option is activated." | ||
| }, | ||
| "tfkmers_model": { | ||
| "type": "string", | ||
| "description": "Path to TransforKmers model. Required if filter activated." | ||
| }, | ||
| "tfkmers_threshold": { | ||
| "type": "integer", | ||
| "description": "TransforKmers prediction threshold below which new transcripts are retained.", | ||
| "default": "0.2", | ||
| "minimum": "0", | ||
| "maximum": "1" | ||
| }, | ||
| "operation": { | ||
| "type": "string", | ||
| "description": "Operation to retained novel transcripts. 'union' retain tx validated by either bambu or transforkmers, 'intersection' retain tx validated by both.", | ||
| "enum": ["union", "intersection"], | ||
| "default": "intersection" | ||
| } | ||
| } | ||
| }, | ||
| "performance_options": { | ||
| "title": "Performance options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-terminal", | ||
| "description": "Parameters related to performance.", | ||
| "properties": { | ||
| "maxCpu": { | ||
| "type": "integer", | ||
| "description": "Max cpu threads used by ANNEXA.", | ||
| "default": "8" | ||
| }, | ||
| "maxMemory": { | ||
| "type": "integer", | ||
| "description": "Max memory (in GB) used by ANNEXA.", | ||
| "default": "40" | ||
| } | ||
| } | ||
| }, | ||
| "nextflow_options": { | ||
| "title": "Nextflow options", | ||
| "type": "object", | ||
| "fa_icon": "fas fa-terminal", | ||
| "description": "Parameters related to Nextflow.", | ||
| "properties": { | ||
| "resume": { | ||
| "description": "Resume task from cached work (useful for recovering from errors when using singularity)." | ||
| }, | ||
| "with-report": { | ||
| "description": "Create an HTML execution report with metrics such as resource usage for each workflow process." | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/defs/required_options" | ||
| }, | ||
| { | ||
| "$ref": "#/defs/profile_options" | ||
| }, | ||
| { | ||
| "$ref": "#/defs/main_options" | ||
| }, | ||
| { | ||
| "$ref": "#/defs/bambu_options" | ||
| }, | ||
| { | ||
| "$ref": "#/defs/filtering_options" | ||
| }, | ||
| { | ||
| "$ref": "#/defs/performance_options" | ||
| }, | ||
| { | ||
| "$ref": "#/defs/nextflow_options" | ||
| } | ||
| ] | ||
| } |