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forward input is not seen by next stage after a parallel branch

Open ssayols opened this issue 5 years ago • 0 comments

Hi there, we realized that since release version 0.9.9.7, forward input seems to be ignored if run as the last step of a parallel branch. Consider this minimal example:

foo = {
    transform(".foo") {
        exec "echo $input > $output"
    }
}

bar = {
    transform(".bar") {
        exec "echo $input > $output"
    }
    forward input
}

foobar = {
    transform(".foobar") {
        exec "echo $input > $output"
    }
}

Bpipe.run {
    "%.txt" * [ foo + bar ] + "%.foo" * [ foobar ]
}

In versions prior to 0.9.9.7 the pattern "%.foo" collects all output files generated by the stage foo (forwarded by bar), while 0.9.9.7 issues a warning and doesn't run foobar at all:

Note: a pattern '%.foo' was provided, but did not match any of the files provided as input [x.bar, y.bar, z.bar].

cheers, Sergi

ssayols avatar Aug 07 '19 11:08 ssayols