search

epigen / scifiRNA-seq

GNU General Public License v3.0
11 stars 5 forks source link

in submit_job cmd = """{cmd} -J {job_name} \\ KeyError: 'job_name' #3

Closed oliclement closed 3 years ago

oliclement commented 3 years ago

Hey André, I ran the scifi map command and ran into the following error:

    map_command(args, sample_name, sample_out_dir, r1_annotation, _CONFIG)
  File "/mnt/remoteserv/switch/userdata/usrdat03/userdata/oclement/Toolbin/Stiletto/miniconda3/envs/scifi/bin/scifiRNA-seq/build/lib/scifi/map.py", line 85, in map_command
    submit_job(job, params)
  File "/mnt/remoteserv/switch/userdata/usrdat03/userdata/oclement/Toolbin/Stiletto/miniconda3/envs/scifi/bin/scifiRNA-seq/build/lib/scifi/job_control.py", line 37, in submit_job
    cmd = """{cmd} -J {job_name} \\
KeyError: 'job_name'

It seems to me that the job_name argument is missing in the map.py script in params (line 69). Currently, line 69 is: params = dict(map_params, job_file=job, log_file=log)

Shouldn't it be ? params = dict(map_params, job_file=job, job_name=job_name, log_file=log)

Similarly, shouldn't it also be changed on line 99?

afrendeiro commented 3 years ago

That seems correct. Could you please submit a PR?