{"action":"opened","issue":{"url":"https://api.github.com/repos/common-workflow-language/common-workflow-language/issues/154","labels_url":"https://api.github.com/repos/common-workflow-language/common-workflow-language/issues/154/labels{/name}","comments_url":"https://api.github.com/repos/common-workflow-language/common-workflow-language/issues/154/comments","events_url":"https://api.github.com/repos/common-workflow-language/common-workflow-language/issues/154/events","html_url":"https://github.com/common-workflow-language/common-workflow-language/issues/154","id":113888170,"number":154,"title":"Specifying \"--outdir\" to cwl-runner when running a Workflow doesn't appear to work","user":{"login":"vardaofthevalier","id":6384889,"avatar_url":"https://avatars.githubusercontent.com/u/6384889?v=3","gravatar_id":"","url":"https://api.github.com/users/vardaofthevalier","html_url":"https://github.com/vardaofthevalier","followers_url":"https://api.github.com/users/vardaofthevalier/followers","following_url":"https://api.github.com/users/vardaofthevalier/following{/other_user}","gists_url":"https://api.github.com/users/vardaofthevalier/gists{/gist_id}","starred_url":"https://api.github.com/users/vardaofthevalier/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vardaofthevalier/subscriptions","organizations_url":"https://api.github.com/users/vardaofthevalier/orgs","repos_url":"https://api.github.com/users/vardaofthevalier/repos","events_url":"https://api.github.com/users/vardaofthevalier/events{/privacy}","received_events_url":"https://api.github.com/users/vardaofthevalier/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-10-28T18:16:51Z","updated_at":"2015-10-28T18:16:51Z","closed_at":null,"body":"When I run one of my CommandLineTools (which runs in a Docker container) using the \"--outdir\" flag, I can see that the output directory gets set correctly:\r\n```\r\nsudo cwl-runner --outdir /cwl-data/workflows/snapr/outputs snapr-index.cwl snapr-index.json\r\n/usr/local/bin/cwl-runner 1.0.20151022085449\r\n[job 52613392] /cwl-data/workflows/snapr/outputs$ docker run -i --volume=/home/abby/bioinformatics-pipelines/cwl-examples/snapr/snapr-index/genome-index/.success:/tmp/job21078165_genome-index/.success:ro --volume=/cwl-data/workflows/snapr/inputs/sequence.fa:/tmp/job21078165_inputs/sequence.fa:ro --volume=/cwl-data/workflows/snapr/outputs:/tmp/job_output:rw --volume=/tmp/tmp0T8fq2:/tmp/job_tmp:rw --workdir=/tmp/job_output --user=0 --rm --env=TMPDIR=/tmp/job_tmp isbbheavner/snapr_1.0dev57_v2 snapr index /tmp/job21078165_inputs/sequence.fa genome-index > /cwl-data/workflows/snapr/outputs/snapr-index.out\r\n\r\n```\r\n\r\nWhen I attempt to run a Workflow using the same CommandLineTool as a step, using the \"--outdir\" flag has no effect:\r\n```\r\nsudo cwl-runner --outdir /cwl-data/workflows/snapr/outputs snapr-pipeline2.cwl snapr-pipeline2.json\r\n/usr/local/bin/cwl-runner 1.0.20151022085449\r\n[job 38991504] /tmp/tmpJHsaiD$ docker run -i --volume=/tmp/tmp1N0uv5/mkdirs.stdout:/tmp/job601370219_tmp1N0uv5/mkdirs.stdout:ro --volume=/cwl-data/workflows/snapr/inputs/sequence.fa:/tmp/job601370219_inputs/sequence.fa:ro --volume=/tmp/tmpJHsaiD:/tmp/job_output:rw --volume=/tmp/tmpSp49V9:/tmp/job_tmp:rw --workdir=/tmp/job_output --user=0 --rm --env=TMPDIR=/tmp/job_tmp isbbheavner/snapr_1.0dev57_v2 snapr index /tmp/job601370219_inputs/sequence.fa genome-index > /tmp/tmpJHsaiD/snapr-index.out\r\n\r\n```\r\nWhat I need is for all of my workflow steps to have access to the same output directory.  Is there some other way to force the output directory to be the same for all workflow steps?"}}