From 96a985d0a5935fb4cff886a7de0c81011673948a Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Wed, 11 Mar 2020 10:02:55 -0400 Subject: [PATCH] Connect stdin/stdout in docker containers. Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- vcf2fasta.go | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/vcf2fasta.go b/vcf2fasta.go index 7b198d4f71..e02f77556c 100644 --- a/vcf2fasta.go +++ b/vcf2fasta.go @@ -187,7 +187,7 @@ func maybeInDocker(args, mountfiles []string) []string { return args } dockerrun := []string{ - "docker", "run", "--rm", + "docker", "run", "--rm", "-i", "--log-driver=none", } for _, f := range mountfiles { @@ -229,6 +229,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error { wg.Add(1) go func() { defer wg.Done() + defer bedw.Close() log.Printf("running %v", bed.Args) err := bed.Run() if err != nil { @@ -249,6 +250,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error { wg.Add(1) go func() { defer wg.Done() + defer bedcompw.Close() log.Printf("running %v", bedcomp.Args) err := bedcomp.Run() if err != nil { -- 2.30.2