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OpenOmics / weave

An awesome BCL demultiplexing and FastQ quality-control pipeline
https://openomics.github.io/weave/
MIT License
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initial Illumnia demultiplexing cli #4

Closed rroutsong closed 1 year ago

rroutsong commented 1 year ago

Building and testing of the dmux run subcommand:

usage: dmux run [-h] [-o Output top directory] [-p] Run directory [Run directory ...]

positional arguments:
  Run directory         Full & complete run id, no wildcards or regex (format YYMMDD_INSTRUMENTID_TIME_FLOWCELLID)

optional arguments:
  -h, --help            show this help message and exit
  -o Output top directory, --output Output top directory
  -p, --pretend

run id positional arguments except both run ids (which map to pre-defined directories) or full paths to runs. It will accept multiple ids or paths (nargs).

executing demultiplexing on a run or multiples will send each of these runs to slurm for dispatching.

the output will look like:

(.venv_fresh) [routsongrm@cn4334 Dmux] {9646546}$ rm -rf /data/RTB_GRS/dev/Dmux/test_demux; dmux run 230907_NS500353_0215_AHLTNVBGXM -o /data/RTB_GRS/dev/Dmux/test_demux
>  Executing demultiplexing of run 230907_NS500353_0215_AHLTNVBGXM...
        > Snakemake job id: 1, slurm job id: 9676947