{"action":"created","issue":{"url":"https://api.github.com/repos/nextflow-io/nextflow/issues/888","repository_url":"https://api.github.com/repos/nextflow-io/nextflow","labels_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/888/labels{/name}","comments_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/888/comments","events_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/888/events","html_url":"https://github.com/nextflow-io/nextflow/issues/888","id":367234882,"node_id":"MDU6SXNzdWUzNjcyMzQ4ODI=","number":888,"title":"nextflow pull not working if nextflow.config is a symbolic link","user":{"login":"zichner","id":10066078,"node_id":"MDQ6VXNlcjEwMDY2MDc4","avatar_url":"https://avatars3.githubusercontent.com/u/10066078?v=4","gravatar_id":"","url":"https://api.github.com/users/zichner","html_url":"https://github.com/zichner","followers_url":"https://api.github.com/users/zichner/followers","following_url":"https://api.github.com/users/zichner/following{/other_user}","gists_url":"https://api.github.com/users/zichner/gists{/gist_id}","starred_url":"https://api.github.com/users/zichner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zichner/subscriptions","organizations_url":"https://api.github.com/users/zichner/orgs","repos_url":"https://api.github.com/users/zichner/repos","events_url":"https://api.github.com/users/zichner/events{/privacy}","received_events_url":"https://api.github.com/users/zichner/received_events","type":"User","site_admin":false},"labels":[{"id":33572980,"node_id":"MDU6TGFiZWwzMzU3Mjk4MA==","url":"https://api.github.com/repos/nextflow-io/nextflow/labels/kind/bug","name":"kind/bug","color":"fc2929","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-10-05T14:26:07Z","updated_at":"2018-10-08T06:57:27Z","closed_at":null,"author_association":"NONE","body":"## Bug report \r\n\r\nIf the actual `nextflow.config` file is not located in the top-level directory of a pipeline repository, but only linked there using a symbolic link, `nextflow pull` (v0.32.0) gives the following error:\r\n\r\n```\r\nERROR ~ Project config file is malformed -- Cause: No signature of method: groovy.util.ConfigObject.div() is applicable for argument types: (ConfigObject) values: [[:]]\r\nPossible solutions: is(java.lang.Object), min(groovy.lang.Closure), wait(), size(), dump(), find()\r\n```\r\n\r\nUsing a symbolic link for `nextflow.config` was working without problems until NF version 0.31.1\r\n\r\nThis is likely related to changes due to #863 \r\n\r\nIs this something that can be fixed or is the use of symbolic links considered an absolute no-go?\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/nextflow-io/nextflow/issues/comments/427736548","html_url":"https://github.com/nextflow-io/nextflow/issues/888#issuecomment-427736548","issue_url":"https://api.github.com/repos/nextflow-io/nextflow/issues/888","id":427736548,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNzczNjU0OA==","user":{"login":"pditommaso","id":816968,"node_id":"MDQ6VXNlcjgxNjk2OA==","avatar_url":"https://avatars0.githubusercontent.com/u/816968?v=4","gravatar_id":"","url":"https://api.github.com/users/pditommaso","html_url":"https://github.com/pditommaso","followers_url":"https://api.github.com/users/pditommaso/followers","following_url":"https://api.github.com/users/pditommaso/following{/other_user}","gists_url":"https://api.github.com/users/pditommaso/gists{/gist_id}","starred_url":"https://api.github.com/users/pditommaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pditommaso/subscriptions","organizations_url":"https://api.github.com/users/pditommaso/orgs","repos_url":"https://api.github.com/users/pditommaso/repos","events_url":"https://api.github.com/users/pditommaso/events{/privacy}","received_events_url":"https://api.github.com/users/pditommaso/received_events","type":"User","site_admin":false},"created_at":"2018-10-08T06:57:27Z","updated_at":"2018-10-08T06:57:27Z","author_association":"MEMBER","body":"The problem is that a symlink is stored as a plain file, eg: \r\n\r\n```\r\n{\r\n\t\"file_name\": \"nextflow.config\",\r\n\t\"file_path\": \"nextflow.config\",\r\n\t\"size\": 20,\r\n\t\"encoding\": \"base64\",\r\n\t\"content_sha256\": \"c50b0d932cf4304d0910e894892b224b825428d23c26f10e824a683b5a7ac90f\",\r\n\t\"ref\": \"master\",\r\n\t\"blob_id\": \"a231dc2ce991cecd261cad3cd2b61362167e8929\",\r\n\t\"commit_id\": \"1c0812064ae361b02c00cc264fbd03473c640766\",\r\n\t\"last_commit_id\": \"60101601ac686221ba9a62da9c3b16161df5af5f\",\r\n\t\"content\": \"Y29uZi9uZXh0Zmxvdy5jb25maWc=\"\r\n}\r\n```\r\n\r\nIf you decode the content: \r\n\r\n```\r\n$ echo \"Y29uZi9uZXh0Zmxvdy5jb25maWc=\" | base64 --decode\r\nconf/nextflow.config\r\n```\r\n\r\nBasically what is happening is that NF tries to interprets the string `conf/nextflow.config` as the config content and therefore reports that error. \r\n\r\nAFAIK the API does not provide a way to know if a file is a symlink. Not sure how this can be solved. Maybe with some heuristic trying to resolve as a path when it *seems* relative paths. But it looks fragile. \r\n\r\nWhy it was working? Because  before #863 the exception was ignored and the content of the manifest was ignored."}}
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