Access to original $input files from command line

[lonsbio]

From [email protected] on 2014-10-11T08:13:56Z

Using the "from" structure I can access outputs from previous stages in the pipeline, but I don't seem to be able to access the original input files.

My pipeline does a number of intermediate calculations using the original input files (in parallel), and then applies the resulting transformation to the original input. Thus, I need the original file name to do this.

Original issue: http://code.google.com/p/bpipe/issues/detail?id=102

[lonsbio]

From [email protected] on 2014-10-10T16:13:32Z

Solved the problem using a branch variable in the first stage branch.origname = "$input"

Then I use $origname at the last stage to use the original input file.

It would be nice if "from" would scan all the way back to the original input files, rather than just up to the first stage.

[gdevenyi]

Reference solution https://github.com/CobraLab/mincbeast_bpipe/blob/master/mincbeast.pipe