How to get created directories out of CWL tmp path

Question

[DT]

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'

Answer 1

[Michael R. Crusoe]

Hello DT.

You should use the InitialWorkDirRequirement to stage the input file into the writeable output directory.

http://www.commonwl.org/v1.0/UserGuide.html#Staging_input_files_in_the_output_directory

[DT]

Hello Michael,

Thank you for your reply.

I tried it, but cwl-runner prepended tmp paths to the directory input and then the wrapped tool cannot find the directory because of the prepend (see log below).

Also, in the 'cannot open file . . .' message below, it's missing a '/' before the file in the directory. It should be '...Run4_forR/hp1.csv'.

Any suggestions? Thanks!!

[job r-MakeBarLibParTables.cwl] /tmp/tmpfE4k3e$ Rscript \
    /home/dz/MakeBarcodeTablesV3.R \
    --dir \
    /tmp/tmpVTGQPt/stg43a89205-59fe-41d5-92ba-df9774192388/Run4_forR

Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/tmp/tmpVTGQPt/stg43a89205-59fe-41d5-92ba-df9774192388/Run4_forRhp1.csv': No such file or directory

[Michael R. Crusoe]

Could be an error with the script, it is normal to specify a directory without a trailing slash

If you absolutely can't fix the Rscript to add the directory separator ('/' on unix) then you will need to add valueFrom: ${ return self + '/'; } to the inputBinding with InlineJavascriptRequirement added to the requirements