sahilseth / funr Goto Github PK

flowr run
try:      flowr -h run     to get more details on this function.
Error in run(wd = opts_flow$get("flow_run_path"), execute = FALSE) :
  Please choose a pipeline to run, from the above list.
Error in funr(args = commandArgs(trailingOnly = TRUE), script_name = "flowr",  :
Execution halted

[root@650ee0cf2924 tmp]# flowr -v ultraseq::merge_sheets x=tumor___normal_1.mutect.txt .filter='judgement=='KEEP'' outfile=tmp.tsv
args:
-vultraseq::merge_sheetsx=tumor___normal_1.mutect.txt.filter=judgement==KEEPoutfile=tmp.tsv
script_args:
-v

using func:
ultraseq::merge_sheets
with final args:
x=tumor___normal_1.mutect.txt.filter=judgement==KEEPoutfile=tmp.tsv
loading pkg: ultraseq
Loading required package: assertthat
ultraseq: genomic flows made faster
args:
$x


$outfile


$.filter
[1] NA

$...



get_params: we have 3 parameters
x=tumor___normal_1.mutect.txt
.filter=judgement==KEEP
outfile=tmp.tsv

starting process with: x=tumor___normal_1.mutect.txt
[1] "tumor___normal_1.mutect.txt"
processed param: x value tumor___normal_1.mutect.txt

starting process with: .filter=judgement==KEEP
[1] "judgement"
processed param: .filter value NA

starting process with: outfile=tmp.tsv
[1] "tmp.tsv"
processed param: outfile value tmp.tsv
$x
[1] "tumor___normal_1.mutect.txt"

$outfile
[1] "tmp.tsv"

$.filter
[1] NA


Starting merge_sheets with params
 x: tumor___normal_1.mutect.txt
outfile: tmp.tsv
.filter: NA
List of 3
 $ x      : chr "tumor___normal_1.mutect.txt"
 $ outfile: chr "tmp.tsv"
 $ .filter: logi NA

[1] "Hi"
Error in path.expand(path) : invalid 'path' argument
Calls: source ... file.path -> <Anonymous> -> normalizePath -> path.expand
Execution halted