Commit f17f564e authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Improved help

parent 7eec04a9
......@@ -2,4 +2,3 @@
*trace*
*dag*
*html*
test*
......@@ -11,38 +11,15 @@ workflow.onError = {
println "Oops .. something went wrong"
}
params.help=false
def usage() {
println("animalerie-wf.nf --in <input_dir> --kronaout <output_krona> --resumeout <output_resume> --annotationout <output_annotation> --cpus <nb_cpus> -w <output_temp>")
println("--in Directory containing fastq files (Single end only). Full path is mandatory")
println("--kronaout Output krona file (default ${HOME}/krona.html)")
println("--resumeout Output resume file (default ${HOME}/resume_table.tsv)")
println("--annotationout Output annotation file (default ${HOME}/annotation_table.tsv)")
println("--countout Output count file (default ${HOME}/count_table.tsv)")
println("--cpus Number of cpus for process (default 2)")
println("-w Temporary output (usually /pasteur/scratch/animalerie-wf)")
println("--identity Read minimum identity with blast in percent (Default 50)")
println("--coverage Read minimum coverage with blast in percent (Default 50)")
println("--identity Read minimum identity with diamond in percent (Default 40)")
println("--coverage Read minimum coverage with diamond in percent (Default 40)")
println("--evalue E-value threshold (Default 1E-3)")
}
if(params.help){
usage()
exit(1)
}
// General parameters
params.in="${baseDir}/test/"
params.cpus = 6
params.mail = "amine.ghozlane@pasteur.fr"
params.kronaout = "${HOME}/krona.html"
params.resumeout = "${HOME}/resume_table.tsv"
params.annotationout = "${HOME}/annotation_table.tsv"
params.countout = "${HOME}/count_table.tsv"
params.out = "${HOME}/"
params.kronaout = "${params.out}/krona.html"
params.resumeout = "${params.out}/resume_table.tsv"
params.annotationout = "${params.out}/annotation_table.tsv"
params.countout = "${params.out}/count_table.tsv"
// Annotation parameters
params.identity = 50
params.dia_identity = 40
......@@ -62,10 +39,36 @@ params.phi = "/local/databases/index/bowtie/2.1.0/phiX.fa"
params.nt = "/local/databases/fasta/nt"
params.taxadb = "/local/databases/rel/taxadb/current/db/taxadb_full.sqlite"
params.nrdb = "/pasteur/scratch/amine/nr.dmnd"
params.out = "$baseDir/"
myDir = file(params.out)
myDir.mkdirs()
params.help=false
def usage() {
println("animalerie-wf.nf --in <input_dir> --out <output_dir> --cpus <nb_cpus>")
println("--in Directory containing fastq files (Single end only, in format .fastq or .fastq.gz, default ${params.in}).")
println("--out Output directory (default ${params.out}). ")
println("--kronaout Output krona file (default ${params.out}krona.html)")
println("--resumeout Output resume file (default ${params.out}resume_table.tsv)")
println("--annotationout Output annotation file (default ${params.out}annotation_table.tsv)")
println("--countout Output count file (default ${params.out}count_table.tsv)")
println("--cpus Number of cpus for process (default ${params.cpus})")
println("-w Temporary output (usually /pasteur/scratch/animalerie-wf)")
println("--identity Read minimum identity with blast in percent (Default ${params.identity})")
println("--coverage Read minimum coverage with blast in percent (Default ${params.coverage})")
println("--identity Read minimum identity with diamond in percent (Default ${params.dia_identity})")
println("--coverage Read minimum coverage with diamond in percent (Default ${params.dia_coverage})")
println("--evalue E-value threshold (Default ${params.evalue})")
}
if(params.help){
usage()
exit(1)
}
/*fastqChannel = Channel.fromPath("${params.in}")
.ifEmpty { exit 1, "Cannot find read file: ${params.in}" }
.splitCsv(sep: "\t")
......
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