Skip to content

Update method1.nf #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gwajnberg wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update method1.nf #1

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 9 additions & 1 deletion method1.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,18 @@ params.move = false // whether or not the original files have to be moved fr
params.datadir = "/mnt/NAS/nanopore_runs/" // location of the raw/original run files
params.outdir = "$HOME/jantest/method1/" // location to collect all output/results
params.publishdir = "${params.outdir}${params.target}/" // location to save files for the current target
params.length_chopper = 1 // default value of the minimum read length to filter out in chopper
params.qcscore_chopper = 0 // default value of the minimum qcscore to filter out in chopper
val(datadir)
val(publishdir)
val(target)
val(length)
val(qcscore)

// Subworkflows
include { MOVEFILES } from './subworkflow/movefiles'
include { CONCAT_RAW_FASTQ } from './subworkflow/concat_raw_fastq'
include { FILTERING } from './subworkflow/filtering'


workflow {
Expand All @@ -30,5 +38,5 @@ workflow {
else {
CONCAT_RAW_FASTQ(params.datadir, params.target, params.publishdir)
}

FILTERING (params.datadir,params.target,params.length_chopper,params.qcscore_chopper
}