{"action":"opened","issue":{"url":"https://api.github.com/repos/EnginesOn/galaxy_tools/issues/3","repository_url":"https://api.github.com/repos/EnginesOn/galaxy_tools","labels_url":"https://api.github.com/repos/EnginesOn/galaxy_tools/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/EnginesOn/galaxy_tools/issues/3/comments","events_url":"https://api.github.com/repos/EnginesOn/galaxy_tools/issues/3/events","html_url":"https://github.com/EnginesOn/galaxy_tools/issues/3","id":177159981,"number":3,"title":"It always used the last else section and fails reading the file","user":{"login":"bimbam23","id":2727580,"avatar_url":"https://avatars.githubusercontent.com/u/2727580?v=3","gravatar_id":"","url":"https://api.github.com/users/bimbam23","html_url":"https://github.com/bimbam23","followers_url":"https://api.github.com/users/bimbam23/followers","following_url":"https://api.github.com/users/bimbam23/following{/other_user}","gists_url":"https://api.github.com/users/bimbam23/gists{/gist_id}","starred_url":"https://api.github.com/users/bimbam23/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bimbam23/subscriptions","organizations_url":"https://api.github.com/users/bimbam23/orgs","repos_url":"https://api.github.com/users/bimbam23/repos","events_url":"https://api.github.com/users/bimbam23/events{/privacy}","received_events_url":"https://api.github.com/users/bimbam23/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-09-15T12:12:16Z","updated_at":"2016-09-15T12:12:16Z","closed_at":null,"body":"This is very strange I selected fastqc (Raw Files) but its using the last Else statement:\r\n\r\n`mkdir` multiqc_WDir; mkdir multiqc_WDir/fastqc_0; cat /opt/galaxy/production/galaxy-dist/database/files/020/dataset_20859.dat > multiqc_WDir/fastqc_0/'FastQC on data 552: RawData'; mkdir multiqc_WDir/fastqc_1; cat /opt/galaxy/production/galaxy-dist/database/files/020/dataset_20857.dat > multiqc_WDir/fastqc_1/'FastQC on data 517: RawData'; mkdir multiqc_WDir/fastqc_2; cat /opt/galaxy/production/galaxy-dist/database/files/020/dataset_20855.dat > multiqc_WDir/fastqc_2/'FastQC on data 516: RawData'; multiqc `multiqc_WDir;`\r\n\r\nif I add an echo $repeat.software file;  somewhere to the code I print fastqc as expected.\r\n"}}
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