reddylab / ggr-cwl-ipynb-gen Goto Github PK

When using sftp, if the data is coming from more than one source (e.g. when the sequencing core sequence one lane in a different day), the script fails. Review https://github.com/alexbarrera/ggr-cwl-ipynb-gen/blob/master/templates/download_fastq_files.j2#L7

The notebook relies heavily on using the same project name than the flowcell sequencing project name, which might not be the case (e.g. if data coming from multiple sources).

The bs command-line program should replace basemount according to the Illumina folks (it is the project they are actively maintaining). Both the flow of execution and syntax changes, so we will need someone to take on implementing the necessary changes to the jinja2 template to download files when --data-from miseq is used. Also the --data-from option should be change from miseq to basespace since the sequencing data will come from both MiSeq and Nextseq sequencers.

The relative import introduced below is producing an error when trying to run ggr-cwl-ipynb-gen.py. It replaces the absolute import import ggr_cwl_ipynb_gen.consts as consts which still works. I guess this was introduced by pylint or linter. We need to add test to avoid these situations.

Traceback (most recent call last):
  File "/data/reddylab/software/miniconda3/envs/alex_py3/bin/ggr-cwl-ipynb-gen.py", line 18, in <module>
    from . import consts
ImportError: attempted relative import with no known parent package

Python 2 is no longer supported. We should make sure this works with Python 3.