Hello,

I have a tool that takes a directory (--dir ~/Run4_forR) with a samples.csv file as input, and the tool creates and outputs a directory of folders and files in the same input directory as shown by tree below. It runs okay normally, but when I wrap it in CWL, it cannot create the directory tree because of the tmp paths prepended by CWL ('/tmp/tmpWCW3do/Run4_forR/L1'). How should I solve this issue? thanks

Command: Rscript /home/dz/MakeBarcodeTablesV3.R --dir ~/Run4_forR/

Output:

  dz@v:~/Run4_forR$ tree
    .
    ├── samples.csv
    ├── L1
    │   ├── barcode1.txt
    │   └── library_params1.txt
    ├── L2
    │   ├── barcode2.txt
    │   └── library_params2.txt
    ├── L3
    │   ├── barcode3.txt
    │   └── library_params3.txt
    ├── L4
    │   ├── barcode4.txt
    │   └── library_params4.txt
    ├── L5
    │   ├── barcode5.txt
    │   └── library_params5.txt
    ├── L6
    │   ├── barcode6.txt
    │   └── library_params6.txt
    ├── L7
    │   ├── barcode7.txt
    │   └── library_params7.txt
    └── L8
        ├── barcode8.txt
        └── library_params8.txt

cwl-runner warnings:

Warning messages: 1: In dir.create(paste(location, "L", l, sep = ""), showWarnings = TRUE, : cannot create dir '/tmp/tmpWCW3do/Run4_forR/L1', reason 'No such file or directory'