Variable substitution in Ruffus decorator?

[lucygarner]

Hi,

Is it possible to perform variable substitution in the Ruffus header - I would like to set the input and output directories based on the .yml file (so that they are not local paths from the cwd).

e.g.

@transform(PARAMS["directory_input"] + "/*/matrix.mtx.gz",
           regex(PARAMS["directory_input"] + r"/(\d{2}_B\d{1})/matrix.mtx.gz"),
           PARAMS["directory_output"] + r"/results/Robjects/\1_seurat_singlet.rds")
def hto_demux(infile, outfile):
    '''Run HTO demux script for individual samples'''

This seems to work but I'm not sure if it is the best way do to it?

Best,
Lucy

[AndreasHeger]

Hi, yes, this should work.Parameters for inputs/outputs in ruffus are just strings (or list of strings) that can be composed any which way.

Not having tested it, but you can probably simplify a little:

@transform(PARAMS["directory_input"] + "/*/matrix.mtx.gz",
           regex(r"/(\d{2}_B\d{1})/matrix.mtx.gz"),
           PARAMS["directory_output"] + r"/results/Robjects/\1_seurat_singlet.rds")
def hto_demux(infile, outfile):
    '''Run HTO demux script for individual samples'''

[lucygarner]

Great thank you, I'll give it a go.

[lucygarner]

Thanks @AndreasHeger. Do you see any way to simplify the following?

@subdivide(tcr_by_donor,
           regex(PARAMS["working_dir"] + 
           r"/results/TCR/(\w+-?\d+)_MAIT_paired_chains.txt"), 
           [PARAMS["working_dir"] + r"/results/TCR/tmp/MAIT_\1_nt.tmp",
           PARAMS["working_dir"] + r"/results/TCR/tmp/MAIT_\1_alpha_nt.tmp",
           PARAMS["working_dir"] + r"/results/TCR/tmp/MAIT_\1_beta_nt.tmp"])