allow sequencing_center to be passed as an optional input to demux_launcher #844
Conversation
…uncher allow sequencing_center to be passed as an optional input to demux_launcher; this allows each job spawning a demux (uploader laptops, etc.) to set the sequencing center at upload time
| - name: sequencing_center | ||
| class: string | ||
| optional: true | ||
| help: Optional- the name of the sequencing center specified in the demultiplexing output (bam files) |
There was a problem hiding this comment.
Note in the help string here that the value should avoid any spaces or special characters? Beats having to escape and support all those scenarios.
There was a problem hiding this comment.
We could process the value passed for sequencing center via util.file.string_to_file_name() in illumina.py?
There was a problem hiding this comment.
I'm not assuming that this yml has access to our python util.file. In fact the runSpec looks a bit more bash-like. I'm not worried about the downstream stuff, I'm more worried about your actual runcmd just below if someone entered a sequencing center like "My Sequencing Center".
There was a problem hiding this comment.
That makes sense. I suppose I'll escape the input in illumina.py just to be safe, and also mention in the help text to avoid spaces and special characters.
…void spaces in the DNAnexus applet demux_launcher spaces may cause issues for the bash-like demux_launcher applet script
With this PR, sequencing_center can be passed as an optional input to the demux_launcher DNAnexus applet; this allows each job spawning a demux (uploader laptops, etc.) to set the sequencing center at upload time