Fix docker mounts.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 6c8ec5fbccdba042b945d2d800d91384429f1e3e..383ef85ca76b5a6ad15c83778082549d995edbe9 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -238,7 +238,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                        return err
                }
                bedcompargs := []string{"bedtools", "complement", "-i", "/dev/stdin", "-g", cmd.genomeFile}
-               bedcompargs = maybeInDocker(bedcompargs, []string{cmd.refFile, infile})
+               bedcompargs = maybeInDocker(bedcompargs, []string{cmd.genomeFile})
                bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
                bedcomp.Stdin = bedr
                bedcomp.Stdout = bedcompw