Error when running on long-read data

[Kyung-TaeLee]

Hi, I am trying to run JAFFAL pipeline using apptainer. Below is commandline I used for unning

apptainer run -B {JAFFA_file_dir} -B {Ref_dir} -B {input_file_dir} docker://davidsongroup/jaffa:latest {JAFFA_file_dir}/JAFFAL.groovy {input_file_dir}/input.fastq.gz

I am getting following error and do not see how I can set up "tools.groovy" for running in the manual.

''' WARN: Error evaluating script /mnt/ix2/Experimental_tools/JAFFA-version-2.3/JAFFA_stages.groovy: A script, requested to be loaded from file '/mnt/ix2/Experimental_tools/JAFFA-version-2.3/tools.groovy', could not be accessed. WARN: Error evaluating script /mnt/ix2/Experimental_tools/JAFFA-version-2.3/JAFFA_stages.groovy: A script, requested to be loaded from file '/mnt/ix2/Experimental_tools/JAFFA-version-2.3/tools.groovy', could not be accessed.

Pipeline Failed!

A variable referred to in your script on line 71, 'filter_transcripts' was not defined.

Please check that all pipeline stages or other variables you have referenced by this name are defined.

''' Thank you for your help in advance.

[olliecheng]

Hi Kyung. Can you provide a bit more information about the specific variables {JAFFA_file_dir}, {input_file_dir}, {JAFFA_file_dir} for me? Is /mnt/ix2/Experimental_tools/JAFFA-version-2.3 a directory on the host machine?

[sigmaclennan]

I'm also getting this error when I try to run JAFFAL with apptainer. I also noticed there is no "tools" directory for JAFFA, which made prepping a non-supported reference genome difficult.