Unverified Commit 4c14d3a8 authored by Todor Kondic's avatar Todor Kondic
Browse files

pcl: pb-lite-driver: Update stage buildccs

Also, add some output to add_ccs2csv.R.
parent 6a09819d
......@@ -16,6 +16,7 @@ SEL_ADDUCTS <- NULL # Change to adducts needed, if a subset of adducts
args <- commandArgs(trailingOnly = T)
fn_config <- args[[1]]
if (!file.exists(fn_config)) stop("Config file",fn_config,"does not exist.")
x <- yaml::yaml.load_file(fn_config)
fn_ccs <- x$ccs_src_path
fn_mf_csv <- args[[2]]
......
......@@ -125,7 +125,7 @@ function build() {
function buildccs() {
header BUILDCCS
(cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$INPUTFILE" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
(cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$MANIF" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
footer BUILDCCS
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment