Commit 4da1272c authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Change default dir

parent bdc1d78c
......@@ -14,14 +14,14 @@ workflow.onError = {
params.help=false
def usage() {
println("blast_approach.nf --in <csv_file> --kronaout <output_krona> --resumeout <output_resume> --annotationout <output_annotation> --cpus <nb_cpus> -w <output_temp>")
println("animalerie-wf.nf --in <csv_file> --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 ${baseDir}/krona.html)")
println("--resumeout Output resume file (default ${baseDir}/resume_table.tsv)")
println("--annotationout Output annotation file (default ${baseDir}/annotation_table.tsv)")
println("--countout Output count file (default ${baseDir}/count_table.tsv)")
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 ${HOME}/count_table.tsv)")
println("--cpus Number of cpus for process (default 2)")
println("-w Temporary output (usually /pasteur/scratch/username)")
println("-w Temporary output (usually /pasteur/scratch/animalerie-wf)")
println("--identity Read minimum identity with blast in percent (Default 50)")
println("--coverage Read minimum coverage with blast in percent (Default 50)")
println("--identity Read minimum identity with diamond in percent (Default 40)")
......@@ -39,10 +39,10 @@ if(params.help){
params.in="${baseDir}/test/"
params.cpus = 6
params.mail = "amine.ghozlane@pasteur.fr"
params.kronaout = "${baseDir}/krona.html"
params.resumeout = "${baseDir}/resume_table.tsv"
params.annotationout = "${baseDir}/annotation_table.tsv"
params.countout = "${baseDir}/count_table.tsv"
params.kronaout = "${HOME}/krona.html"
params.resumeout = "${HOME}/resume_table.tsv"
params.annotationout = "${HOME}/annotation_table.tsv"
params.countout = "${HOME}/count_table.tsv"
// Annotation parameters
params.identity = 50
params.dia_identity = 40
......
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