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convert to DSL2
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‎main.nf‎

Lines changed: 79 additions & 111 deletions
Original file line numberDiff line numberDiff line change
@@ -11,53 +11,35 @@
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https://github.com/maxulysse/compile-latex
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--------------------------------------------------------------------------------
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@Documentation
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https://github.com/maxulysse/compile-latex/blob/master/README.md
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https://github.com/maxulysse/compile-latex/blob/main/README.md
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--------------------------------------------------------------------------------
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@Licence
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https://github.com/maxulysse/compile-latex/blob/master/LICENSE
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https://github.com/maxulysse/compile-latex/blob/main/LICENSE
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--------------------------------------------------------------------------------
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Process overview
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- RunXelatex
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- RUNXELATEX
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Run xelatex, optionally biber and xelatex and finally xelatex again
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================================================================================
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= C O N F I G U R A T I O N =
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================================================================================
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*/
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if (params.help) exit 0, helpMessage()
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if (!params.tex) exit 1, 'No tex file, see --help for more information'
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biblio = file(params.biblio)
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pictures = file(params.pictures)
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tex = Channel.fromPath(params.tex)
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/*
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================================================================================
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= P R O C E S S =
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================================================================================
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*/
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startMessage()
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process RunXelatex {
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tag {tex}
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process RUNXELATEX {
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tag { tex }
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publishDir params.outdir, mode: 'link'
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input:
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file biblio
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file pictures
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file tex
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path biblio
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path pictures
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path tex
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output:
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file("*.pdf") into pdf
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path "*.pdf", emit: pdf
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script:
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notes = params.notes == '' ? "" : "\"\\PassOptionsToClass{notes}{beamer}\\input{$tex}\""
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notes = params.notes_only == '' ? notes : "\"\\PassOptionsToClass{notes=only}{beamer}\\input{$tex}\""
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xelatexScript = notes == '' ? "xelatex -shell-escape ${tex}" : "xelatex -shell-escape ${notes}"
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biberScript = biblio.exists() ? "biber ${tex.baseName}.bcf ; ${xelatexScript}" : ""
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renameScript = params.outname == '' ? "" : "cp ${tex.baseName}.pdf ${params.outname}"
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notes = params.notes ? "\"\\PassOptionsToClass{notes}{beamer}\\input{${tex}}\"" : ""
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notes = params.notes_only ? notes : "\"\\PassOptionsToClass{notes=only}{beamer}\\input{${tex}}\""
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xelatexScript = notes ? "xelatex -shell-escape ${tex}" : "xelatex -shell-escape ${notes}"
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biberScript = biblio.exists() ? "biber ${tex.baseName}.bcf ; ${xelatexScript}" : ""
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renameScript = params.outname ? "cp ${tex.baseName}.pdf ${params.outname}" : ""
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"""
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${xelatexScript}
@@ -67,98 +49,84 @@ process RunXelatex {
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"""
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}
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52+
workflow {
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if (params.help) {
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log.info(helpMessage())
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exit(0)
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}
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if (!params.tex) {
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log.error('No tex file, see --help for more information')
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exit(1)
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}
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// Display start message
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compileLatex_ascii()
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minimalInformationMessage()
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// Create input channels
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biblio_ch = Channel.fromPath(params.biblio)
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pictures_ch = Channel.fromPath(params.pictures)
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tex_ch = Channel.fromPath(params.tex)
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// Run the main process
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RUNXELATEX(biblio_ch, pictures_ch, tex_ch)
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}
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/*
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================================================================================
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= F U N C T I O N S =
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================================================================================
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*/
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def compileLatex_ascii() {
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println ""
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println " _.-´`-._ _ _ _ _"
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println " _.-´ T X `-._ (_) | | | | |"
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println "|`-._ E _.-´| ___ ___ _ __ ___ _ __ _| | ___ | | __ _| |_ _____ __"
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println "|--. `-.__.-´ . | / __/ _ \\| '_ ` _ \\| '_ \\| | |/ _ \\___| |/ _` | __/ _ \\ \\/ /"
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println "| \\.---| . | | | | (_| (_) | | | | | | |_) | | | __/___| | (_| | || __/> <"
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println "|---´\\ | | | | | \\___\\___/|_| |_| |_| .__/|_|_|\\___| |_|\\__,_|\\__\\___/_/\\_\\"
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println " `-._ `--| | '_.-´ | |"
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println " `-._|_.-´ |_|"
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println ""
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}
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def compileLatexMessage() {
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// Display compile-latex message
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log.info "compile-latex ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [$workflow.commitId]" : "")
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}
93-
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def grabRevision() {
95-
// Return the same string executed from github or not
96-
return workflow.revision ?: workflow.commitId ?: workflow.scriptId.substring(0,10)
82+
println("")
83+
println(" _.-´`-._ _ _ _ _")
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println(" _.-´ T X `-._ (_) | | | | |")
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println("|`-._ E _.-´| ___ ___ _ __ ___ _ __ _| | ___ | | __ _| |_ _____ __")
86+
println("|--. `-.__.-´ . | / __/ _ \\| '_ ` _ \\| '_ \\| | |/ _ \\___| |/ _` | __/ _ \\ \\/ /")
87+
println("| \\.---| . | | | | (_| (_) | | | | | | |_) | | | __/___| | (_| | || __/> <")
88+
println("|---´\\ | | | | | \\___\\___/|_| |_| |_| .__/|_|_|\\___| |_|\\__,_|\\__\\___/_/\\_\\")
89+
println(" `-._ `--| | '_.-´ | |")
90+
println(" `-._|_.-´ |_|")
91+
println("")
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println("compile-latex ~ ${workflow.manifest.version}")
9793
}
9894

9995
def helpMessage() {
10096
// Display help message
101-
this.compileLatexMessage()
102-
log.info " Usage:"
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log.info " nextflow run maxulysse/compile-latex --tex <input.tex>"
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log.info " --tex"
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log.info " Compile the given tex file"
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log.info " --biblio"
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log.info " Specify the bibliography"
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log.info " Default: biblio.bib"
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log.info " --notes"
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log.info " Generate notes with presentation"
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log.info " --pictures"
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log.info " Specify in which directory are the pictures"
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log.info " Default: pictures/"
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log.info " --tag"
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log.info " Specify with tag to use for the docker container"
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log.info " --outname"
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log.info " Specify output name"
118-
log.info " --outdir"
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log.info " Specify output directory"
120-
log.info " --help"
121-
log.info " You're reading it"
97+
log.info(" Usage:")
98+
log.info(" nextflow run maxulysse/compile-latex --tex <input.tex>")
99+
log.info(" --tex")
100+
log.info(" Compile the given tex file")
101+
log.info(" --biblio")
102+
log.info(" Specify the bibliography")
103+
log.info(" Default: biblio.bib")
104+
log.info(" --notes")
105+
log.info(" Generate notes with presentation")
106+
log.info(" --pictures")
107+
log.info(" Specify in which directory are the pictures")
108+
log.info(" Default: pictures/")
109+
log.info(" --tag")
110+
log.info(" Specify with tag to use for the docker container")
111+
log.info(" --outname")
112+
log.info(" Specify output name")
113+
log.info(" --outdir")
114+
log.info(" Specify output directory")
115+
log.info(" --help")
116+
log.info(" You're reading it")
122117
}
123118

124119
def minimalInformationMessage() {
125120
// Minimal information message
126-
log.info "Command Line: " + workflow.commandLine
127-
log.info "Launch Dir : " + workflow.launchDir
128-
log.info "Work Dir : " + workflow.workDir
129-
log.info "Container : " + workflow.container
130-
log.info "Tex file(s) : " + params.tex
131-
if (biblio.exists()) log.info "Bibliography: " + params.biblio
132-
if (pictures.exists()) log.info "Pictures in : " + params.pictures
133-
}
134-
135-
def nextflowMessage() {
136-
// Nextflow message (version + build)
137-
log.info "N E X T F L O W ~ version " + workflow.nextflow.version + " " + workflow.nextflow.build
138-
}
139-
140-
def startMessage() {
141-
// Display start message
142-
this.compileLatex_ascii()
143-
this.compileLatexMessage()
144-
this.minimalInformationMessage()
145-
}
146-
147-
workflow.onComplete {
148-
// Display end message
149-
this.nextflowMessage()
150-
this.compileLatexMessage()
151-
this.minimalInformationMessage()
152-
log.info "Completed at: " + workflow.complete
153-
log.info "Duration : " + workflow.duration
154-
log.info "Success : " + workflow.success
155-
log.info "Exit status : " + workflow.exitStatus
156-
log.info "Error report: " + (workflow.errorReport ?: '-')
157-
}
158-
159-
workflow.onError {
160-
// Display error message
161-
this.nextflowMessage()
162-
this.compileLatexMessage()
163-
log.info "Workflow execution stopped with the following message: " + $workflow.errorMessage
121+
log.info("Command Line: " + workflow.commandLine)
122+
log.info("Launch Dir : " + workflow.launchDir)
123+
log.info("Work Dir : " + workflow.workDir)
124+
log.info("Container : " + workflow.container)
125+
log.info("Tex file(s) : " + params.tex)
126+
if (file(params.biblio).exists()) {
127+
log.info("Bibliography: " + params.biblio)
128+
}
129+
if (file(params.pictures).exists()) {
130+
log.info("Pictures in : " + params.pictures)
131+
}
164132
}

‎sample.pdf‎

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