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Adding nextflow_schema.json and carrying on
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@toniher
toniher committed Oct 10, 2024
1 parent 5ecca74 commit be9114a
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102 changes: 58 additions & 44 deletions main.nf
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/*
* Copyright (c) 2019-2020, Centre for Genomic Regulation (CRG)
* Copyright (c) 2019-2024, Centre for Genomic Regulation (CRG)
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
Expand All @@ -17,10 +17,13 @@ ExOrthist pipeline for Bioinformatics Core @ CRG
@authors
Luca Cozzuto <[email protected]>
Federica Mantica <[email protected]>
Toni Hermoso Pulido <[email protected]>
===========================================================
*/

version = '0.1'
nextflow.enable.dsl=2

version = '2.0.0'

/*
* Input parameters:
Expand All @@ -30,51 +33,62 @@ params.help = false
params.resume = false


log.info """
╔╦╗┬ ┬┌─┐ ╔═╗─┐ ┬╔═╗┬─┐┌┬┐┬ ┬┬┌─┐┌┬┐
║ ├─┤├┤ ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
╩ ┴ ┴└─┘ ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
==============================================================================
annotations (GTF files) : ${params.annotations}
genomes (fasta files) : ${params.genomes}
cluster file (txt files) : ${params.cluster}
pairwise evo distances : ${params.evodists}
long distance parameters : ${params.long_dist}
medium distance parameters : ${params.medium_dist}
short distance parameters : ${params.short_dist}
pre-computed alignments : ${params.prevaln}
alignment number : ${params.alignmentnum}
orthogroup number : ${params.orthogroupnum}
extraexons (e.g. from VastDB) : ${params.extraexons}
bona fide orthologous exon pairs : ${params.bonafide_pairs}
orthopairs : ${params.orthopairs}
output (output folder) : ${params.output}
email for notification : ${params.email}
INFORMATION ABOUT OPTIONS:
The long, medium, short distance cut-offs are in the format: "int_num;ex_seq;ex_len;prot_sim".
Only exon matches respecting all cut-offs are considered homologous.
- int_num (0,1,2): Number of surrounding intron positions required to be conserved.
- ex_seq (from 0 to 1): Minimum sequence similarity % between a
pair of homologous exons and their corresponding upstream and
downstream exons.
- ex_len (from 0 to 1): Maximum size difference between two homologous exons
(as a fraction of either exon).
- prot_sim (from 0 to 1): Minimum sequence similarity over the entire pairwise alignment
for a pair of protein isoforms to be considered for comparison.
See online README at https://github.com/biocorecrg/ExOrthist for further information about the options.
"""

if (params.help) {
log.info """ExOrthist v2.0.0"""
log.info """ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales.\n"""
exit 1
// log.info """
//
// ╔╦╗┬ ┬┌─┐ ╔═╗─┐ ┬╔═╗┬─┐┌┬┐┬ ┬┬┌─┐┌┬┐
// ║ ├─┤├┤ ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
// ╩ ┴ ┴└─┘ ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
//
// ==============================================================================
// annotations (GTF files) : ${params.annotations}
// genomes (fasta files) : ${params.genomes}
// cluster file (txt files) : ${params.cluster}
// pairwise evo distances : ${params.evodists}
// long distance parameters : ${params.long_dist}
// medium distance parameters : ${params.medium_dist}
// short distance parameters : ${params.short_dist}
// pre-computed alignments : ${params.prevaln}
// alignment number : ${params.alignmentnum}
// orthogroup number : ${params.orthogroupnum}
// extraexons (e.g. from VastDB) : ${params.extraexons}
// bona fide orthologous exon pairs : ${params.bonafide_pairs}
// orthopairs : ${params.orthopairs}
// output (output folder) : ${params.output}
// email for notification : ${params.email}
//
// INFORMATION ABOUT OPTIONS:
// The long, medium, short distance cut-offs are in the format: "int_num;ex_seq;ex_len;prot_sim".
// Only exon matches respecting all cut-offs are considered homologous.
// - int_num (0,1,2): Number of surrounding intron positions required to be conserved.
// - ex_seq (from 0 to 1): Minimum sequence similarity % between a
// pair of homologous exons and their corresponding upstream and
// downstream exons.
// - ex_len (from 0 to 1): Maximum size difference between two homologous exons
// (as a fraction of either exon).
// - prot_sim (from 0 to 1): Minimum sequence similarity over the entire pairwise alignment
// for a pair of protein isoforms to be considered for comparison.
//
// See online README at https://github.com/biocorecrg/ExOrthist for further information about the options.
// """
//
// if (params.help) {
// log.info """ExOrthist v2.0.0"""
// log.info """ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales.\n"""
// exit 1
// }

// Load the schema
params = new nextflow.script.ScriptBinding().getParams()
def schema = new File("$projectDir/nextflow_schema.json")
if (schema.exists()) {
params = new groovy.json.JsonSlurper().parse(schema).properties.params
}


if (params.resume) exit 1, "Are you making the classical --resume typo? Be careful!!!! ;)"



if( !workflow.resume ) {
println "Removing the output folder"
new File("${params.output}").delete()
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128 changes: 128 additions & 0 deletions nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/biocorecrg/exorthist/master/nextflow_schema.json",
"title": "ExOrthist pipeline parameters",
"description": "Schema for the parameters of your ExOrthist pipeline",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/Output Options",
"type": "object",
"required": [
"annotations",
"genomes",
"cluster",
"output"
],
"properties": {
"annotations": {
"type": "string",
"description": "Path to GTF annotation files",
"format": "file-path"
},
"genomes": {
"type": "string",
"description": "Path to fasta genome files",
"format": "file-path"
},
"cluster": {
"type": "string",
"description": "Path to cluster file (txt files)",
"format": "file-path"
},
"output": {
"type": "string",
"description": "Output folder path",
"format": "directory-path"
}
}
},
"analysis_parameters": {
"title": "Analysis Parameters",
"type": "object",
"required": [
"evodists",
"long_dist",
"medium_dist",
"short_dist"
],
"properties": {
"evodists": {
"type": "string",
"description": "Path to a file with pairwise evolutionary distances",
"format": "file-path"
},
"long_dist": {
"type": "string",
"description": "Long distance parameters"
},
"medium_dist": {
"type": "string",
"description": "Medium distance parameters"
},
"short_dist": {
"type": "string",
"description": "Short distance parameters"
},
"prevaln": {
"type": "string",
"description": "Pre-computed alignments"
},
"alignmentnum": {
"type": "integer",
"description": "Alignment number"
},
"orthogroupnum": {
"type": "integer",
"description": "Orthogroup number"
}
}
},
"additional_data": {
"title": "Additional Data",
"type": "object",
"properties": {
"extraexons": {
"type": "string",
"description": "Extra exons (e.g. from VastDB)",
"format": "file-path"
},
"bonafide_pairs": {
"type": "string",
"description": "Bona fide orthologous exon pairs",
"format": "file-path"
},
"orthopairs": {
"type": "string",
"description": "Orthopairs",
"format": "file-path"
}
}
},
"notification_options": {
"title": "Notification Options",
"type": "object",
"properties": {
"email": {
"type": "string",
"description": "Email for notification",
"format": "email"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/analysis_parameters"
},
{
"$ref": "#/definitions/additional_data"
},
{
"$ref": "#/definitions/notification_options"
}
]
}

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