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build-ctat.nf
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build-ctat.nf
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#!/usr/bin/env nextflow
/*
================================================================================
nf-core/rnafusion
================================================================================
nf-core/rnafusion:
RNA-seq analysis pipeline for detection gene-fusions
--------------------------------------------------------------------------------
@Homepage
https://nf-co.re/rnafusion
--------------------------------------------------------------------------------
@Documentation
https://nf-co.re/rnafusion/docs
--------------------------------------------------------------------------------
@Repository
https://github.com/nf-core/rnafusion
--------------------------------------------------------------------------------
*/
def helpMessage() {
log.info nfcoreHeader()
log.info"""
Usage:
The typical command for downloading references is as follows:
nextflow run nf-core/rnafusion/build-ctat.nf -profile [PROFILE] [OPTIONS] --outdir /path/to/output
Mandatory arguments:
--fasta [file] Path to fasta reference
--gtf [file] Path to GTF annotation
--outdir [path] Output directory for downloading
-profile [str] Configuration profile [https://github.com/nf-core/configs]
""".stripIndent()
}
/*
* SET UP CONFIGURATION VARIABLES
*/
// Show help message
if (params.help) exit 0, helpMessage()
params.fasta = params.genome ? params.genomes[params.genome].fasta ?: null : null
params.gtf = params.genome ? params.genomes[params.genome].gtf ?: null : null
ch_fasta = Channel.value(file(params.fasta)).ifEmpty{exit 1, "Fasta file not found: ${params.fasta}"}
ch_gtf = Channel.value(file(params.gtf)).ifEmpty{exit 1, "GTF annotation file not found: ${params.gtf}"}
if (!params.outdir) exit 1, "Output directory not specified!"
// Header log info
log.info nfcoreHeader()
def summary = [:]
summary['Pipeline Name'] = 'nf-core/rnafusion/build-ctat.nf'
summary['Pipeline Version'] = workflow.manifest.version
if(workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
summary['Output dir'] = params.outdir
summary['User'] = workflow.userName
log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
log.info "\033[2m----------------------------------------------------\033[0m"
// Check the hostnames against configured profiles
checkHostname()
/*
================================================================================
DOWNLOAD
================================================================================
*/
process star_fusion {
label 'process_high'
label 'process_long'
publishDir "${params.outdir}", mode: 'copy'
input:
file(fasta) from ch_fasta
file(gtf) from ch_gtf
output:
file '*'
script:
"""
wget -N ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_releases/Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
wget https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases/download/v0.2.0/fusion_lib.Mar2019.dat.gz -O CTAT_HumanFusionLib.dat.gz
# Dfam
wget https://www.dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm
wget https://www.dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3f
wget https://www.dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3i
wget https://www.dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m
wget https://www.dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p
export TMPDIR=/tmp
prep_genome_lib.pl \\
--genome_fa ${fasta} \\
--gtf ${gtf} \\
--annot_filter_rule /opt/conda/envs/nf-core-rnafusion-star-fusion_1.8.1/ctat-genome-lib-builder-2830cd708c5bb9353878ca98069427e83acdd625/AnnotFilterRuleLib/AnnotFilterRule.pm \\
--fusion_annot_lib CTAT_HumanFusionLib.dat.gz \\
--pfam_db Pfam-A.hmm \\
--dfam_db homo_sapiens_dfam.hmm \\
--CPU ${task.cpus}
"""
}
/*
* Completion
*/
workflow.onComplete {
log.info "[nf-core/rnafusion/build-ctat.nf] Pipeline Complete"
}
def nfcoreHeader() {
// Log colors ANSI codes
c_black = params.monochrome_logs ? '' : "\033[0;30m";
c_blue = params.monochrome_logs ? '' : "\033[0;34m";
c_cyan = params.monochrome_logs ? '' : "\033[0;36m";
c_dim = params.monochrome_logs ? '' : "\033[2m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_reset = params.monochrome_logs ? '' : "\033[0m";
c_white = params.monochrome_logs ? '' : "\033[0;37m";
c_yellow = params.monochrome_logs ? '' : "\033[0;33m";
return """ -${c_dim}--------------------------------------------------${c_reset}-
${c_green},--.${c_black}/${c_green},-.${c_reset}
${c_blue} ___ __ __ __ ___ ${c_green}/,-._.--~\'${c_reset}
${c_blue} |\\ | |__ __ / ` / \\ |__) |__ ${c_yellow}} {${c_reset}
${c_blue} | \\| | \\__, \\__/ | \\ |___ ${c_green}\\`-._,-`-,${c_reset}
${c_green}`._,._,\'${c_reset}
${c_purple} nf-core/rnafusion v${workflow.manifest.version}${c_reset}
-${c_dim}--------------------------------------------------${c_reset}-
""".stripIndent()
}
def checkHostname() {
def c_reset = params.monochrome_logs ? '' : "\033[0m"
def c_white = params.monochrome_logs ? '' : "\033[0;37m"
def c_red = params.monochrome_logs ? '' : "\033[1;91m"
def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
if (params.hostnames) {
def hostname = "hostname".execute().text.trim()
params.hostnames.each { prof, hnames ->
hnames.each { hname ->
if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
log.error "====================================================\n" +
" ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
" but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
" ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
"============================================================"
}
}
}
}
}