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main.nf
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#!/usr/bin/env nextflow
/*
================================================================================
= C O M P I L E - L A T E X =
================================================================================
@Author
Maxime Garcia <[email protected]> [@MaxUlysse]
--------------------------------------------------------------------------------
@Homepage
https://github.com/MaxUlysse/compile-latex
--------------------------------------------------------------------------------
@Documentation
https://github.com/MaxUlysse/compile-latex/blob/master/README.md
--------------------------------------------------------------------------------
@Licence
https://github.com/MaxUlysse/compile-latex/blob/master/LICENSE
--------------------------------------------------------------------------------
Process overview
- RunXelatex
Run xelatex, optionally biber and xelatex and finally xelatex again
================================================================================
= C O N F I G U R A T I O N =
================================================================================
*/
if (params.help) exit 0, helpMessage()
if (!params.tex) exit 1, 'No tex file, see --help for more information'
biblio = file(params.biblio)
pictures = file(params.pictures)
tex = Channel.fromPath(params.tex)
/*
================================================================================
= P R O C E S S =
================================================================================
*/
startMessage()
process RunXelatex {
tag {tex}
publishDir params.outDir, mode: 'link'
input:
file biblio
file pictures
file tex
output:
file("*.pdf") into pdf
script:
notes = params.notes == '' ? "" : "\"\\PassOptionsToClass{notes}{beamer}\\input{$tex}\""
notes = params.notesOnly == '' ? notes : "\"\\PassOptionsToClass{notes=only}{beamer}\\input{$tex}\""
xelatexScript = notes == '' ? "xelatex -shell-escape ${tex}" : "xelatex -shell-escape ${notes}"
biberScript = biblio.exists() ? "biber ${tex.baseName}.bcf ; ${xelatexScript}" : ""
renameScript = params.outName == '' ? "" : "cp ${tex.baseName}.pdf ${params.outName}"
"""
${xelatexScript}
${biberScript}
${xelatexScript}
${renameScript}
"""
}
/*
================================================================================
= F U N C T I O N S =
================================================================================
*/
def compileLatex_ascii() {
println ""
println " _.-´`-._ _ _ _ _"
println " _.-´ T X `-._ (_) | | | | |"
println "|`-._ E _.-´| ___ ___ _ __ ___ _ __ _| | ___ | | __ _| |_ _____ __"
println "|--. `-.__.-´ . | / __/ _ \\| '_ ` _ \\| '_ \\| | |/ _ \\___| |/ _` | __/ _ \\ \\/ /"
println "| \\.---| . | | | | (_| (_) | | | | | | |_) | | | __/___| | (_| | || __/> <"
println "|---´\\ | | | | | \\___\\___/|_| |_| |_| .__/|_|_|\\___| |_|\\__,_|\\__\\___/_/\\_\\"
println " `-._ `--| | '_.-´ | |"
println " `-._|_.-´ |_|"
println ""
}
def compileLatexMessage() {
// Display compile-latex message
log.info "compile-latex ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [$workflow.commitId]" : "")
}
def grabRevision() {
// Return the same string executed from github or not
return workflow.revision ?: workflow.commitId ?: workflow.scriptId.substring(0,10)
}
def helpMessage() {
// Display help message
this.compileLatexMessage()
log.info " Usage:"
log.info " nextflow run MaxUlysse/compile-latex --tex <input.tex>"
log.info " --tex"
log.info " Compile the given tex file"
log.info " --biblio"
log.info " Specify the bibliography"
log.info " Default: biblio.bib"
log.info " --notes"
log.info " Generate notes with presentation"
log.info " --pictures"
log.info " Specify in which directory are the pictures"
log.info " Default: pictures/"
log.info " --tag"
log.info " Specify with tag to use for the docker container"
log.info " --outName"
log.info " Specify output name"
log.info " --outDir"
log.info " Specify output directory"
log.info " --help"
log.info " You're reading it"
}
def minimalInformationMessage() {
// Minimal information message
log.info "Command Line: " + workflow.commandLine
log.info "Launch Dir : " + workflow.launchDir
log.info "Work Dir : " + workflow.workDir
log.info "Container : " + workflow.container
log.info "Tex file(s) : " + params.tex
if (biblio.exists()) log.info "Bibliography: " + params.biblio
if (pictures.exists()) log.info "Pictures in : " + params.pictures
}
def nextflowMessage() {
// Nextflow message (version + build)
log.info "N E X T F L O W ~ version " + workflow.nextflow.version + " " + workflow.nextflow.build
}
def startMessage() {
// Display start message
this.compileLatex_ascii()
this.compileLatexMessage()
this.minimalInformationMessage()
}
workflow.onComplete {
// Display end message
this.nextflowMessage()
this.compileLatexMessage()
this.minimalInformationMessage()
log.info "Completed at: " + workflow.complete
log.info "Duration : " + workflow.duration
log.info "Success : " + workflow.success
log.info "Exit status : " + workflow.exitStatus
log.info "Error report: " + (workflow.errorReport ?: '-')
}
workflow.onError {
// Display error message
this.nextflowMessage()
this.compileLatexMessage()
log.info "Workflow execution stopped with the following message: " + $workflow.errorMessage
}