Input specific output filenames

Question

[nmaki]

I'm working on an implementation of a fastqc wrapper written in CWL, and am wondering if there is a better way to ensure that the log outputs of my script are unique (instead of having to name them manually).

outputs: 
  output_qc_report_file
    type: File
    outputBinding:
      glob: "*_fastqc.zip"
  console_log:
    type: stdout
  error_log:
    type: stderr

Instead of fastqc_con.txt for console log, it would be something like "sample_id-tool_ran.txt" or "22_TO_04_S38_R2_001-fastqc_con.txt.

[Mensur Dlakic]

Don't know about the exact capabilities of CWL, but adding .log to the name of your sample is one of common solutions. Adding a time stamp would be another.

Answer 1

[Tom]

See https://www.commonwl.org/user_guide/05-stdout/index.html

You can choose any name you want for the file created from stdout. Using a javascript expression, you can easily derive the name from other parameters. For your case (using an inputs section i made up) this might look like

inputs:
  reads:
    type: File
    inputBinding:
      position: 2
outputs: 
  output_qc_report_file
    type: File
    outputBinding:
      glob: "*_fastqc.zip"
  console_log:
    type: stdout
stdout: $((inputs.reads.nameroot)+"_console_log.txt")

Just in case it is useful to you: Here is a fastqc tool wrapper i use. However, it does not capture stdout.

[Michael R. Crusoe]

A simpler variation of the stdout:

stdout: $(inputs.reads.nameroot)_console_log.txt

[nmaki]

Thank you for the response! It has helped a bit, I now get a complete run of my script with fastqc and log output. I ended using something similar to the solution you posted:

stdout: $((inputs.seqfile.basename)+"_console_log.txt")

However, the logs themselves are named undefined_console_log.txt and undefined_error_log.txt respectively.

[Tom]

Please post the complete tool, i'm sure we can solve this.

[nmaki]

Since the code is too long to write out, and copy and pasting is giving me formatting errors, I am going to post screenshots of it

https://photos.app.goo.gl/5PERRYeA9m11qT126

Thank you for your help, I really appreciate it!

[Tom]

Hi again!

inputs.seqfile is an array. While the elements in the array probably have a basename, the array itself does not. Would taking the name of the first file in the array be sufficient for your purposes?

inputs.seqfile[0].basename

Also note that basename includes the file extension, so the output would be something like "mysequence.fastq_console_log.txt". You can use nameroot to get the name without the extension.

Cheers, Tom

[nmaki]

Thank you so much, that works perfectly! I'll be integrating this into all of my workflows right away.