{"action":"created","issue":{"url":"https://api.github.com/repos/epam/pipeline-builder/issues/15","repository_url":"https://api.github.com/repos/epam/pipeline-builder","labels_url":"https://api.github.com/repos/epam/pipeline-builder/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/epam/pipeline-builder/issues/15/comments","events_url":"https://api.github.com/repos/epam/pipeline-builder/issues/15/events","html_url":"https://github.com/epam/pipeline-builder/issues/15","id":225444265,"number":15,"title":"WGS Workflow not parsing in Pipeline Builder","user":{"login":"jsotobroad","id":13023616,"avatar_url":"https://avatars3.githubusercontent.com/u/13023616?v=3","gravatar_id":"","url":"https://api.github.com/users/jsotobroad","html_url":"https://github.com/jsotobroad","followers_url":"https://api.github.com/users/jsotobroad/followers","following_url":"https://api.github.com/users/jsotobroad/following{/other_user}","gists_url":"https://api.github.com/users/jsotobroad/gists{/gist_id}","starred_url":"https://api.github.com/users/jsotobroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsotobroad/subscriptions","organizations_url":"https://api.github.com/users/jsotobroad/orgs","repos_url":"https://api.github.com/users/jsotobroad/repos","events_url":"https://api.github.com/users/jsotobroad/events{/privacy}","received_events_url":"https://api.github.com/users/jsotobroad/received_events","type":"User","site_admin":false},"labels":[{"id":572243148,"url":"https://api.github.com/repos/epam/pipeline-builder/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-05-01T14:30:41Z","updated_at":"2017-05-22T12:57:37Z","closed_at":null,"body":"There is a wdl we regularly run but it errors out with this message when trying to `Build`.\r\n`Context initialization failed due to Error: In scatter body keys [workflowoutputs, meta, parametermeta, declaration] are not allowed`.\r\n\r\nThe wdl can be found here - https://github.com/broadinstitute/wdl/blob/develop/scripts/broad_pipelines/PublicPairedSingleSampleWf_170412.wdl\r\n\r\nThere are two scatters in that wdl\r\n```\r\nscatter (unmapped_bam in flowcell_unmapped_bams) {\r\n  \r\n    # Because of a wdl/cromwell bug this is not currently valid so we have to sub(sub()) in each task\r\n    # String base_name = sub(sub(unmapped_bam, \"gs://.*/\", \"\"), unmapped_bam_suffix + \"$\", \"\")\r\n\r\n    String sub_strip_path = \"gs://.*/\"\r\n    String sub_strip_unmapped = unmapped_bam_suffix + \"$\"\r\n\r\n    # QC the unmapped BAM \r\n    call CollectQualityYieldMetrics {\r\n      input:\r\n        input_bam = unmapped_bam,\r\n        metrics_filename = sub(sub(unmapped_bam, sub_strip_path, \"\"), sub_strip_unmapped, \"\") + \".unmapped.quality_yield_metrics\",\r\n        disk_size = flowcell_small_disk,\r\n        preemptible_tries = preemptible_tries\r\n    }\r\n...\r\n```\r\nand\r\n```\r\nscatter (subgroup in CreateSequenceGroupingTSV.sequence_grouping) {\r\n    # Generate the recalibration model by interval\r\n    call BaseRecalibrator {\r\n      input:\r\n        input_bam = SortAndFixSampleBam.output_bam,\r\n        input_bam_index = SortAndFixSampleBam.output_bam_index,\r\n        recalibration_report_filename = base_file_name + \".recal_data.csv\",\r\n        sequence_group_interval = subgroup,\r\n        dbSNP_vcf = dbSNP_vcf,\r\n        dbSNP_vcf_index = dbSNP_vcf_index,\r\n        known_indels_sites_VCFs = known_indels_sites_VCFs,\r\n        known_indels_sites_indices = known_indels_sites_indices,\r\n        ref_dict = ref_dict,\r\n        ref_fasta = ref_fasta,\r\n        ref_fasta_index = ref_fasta_index,\r\n        disk_size = agg_small_disk,\r\n        preemptible_tries = agg_preemptible_tries\r\n    }  \r\n  }  \r\n  \r\n  # Merge the recalibration reports resulting from by-interval recalibration\r\n  call GatherBqsrReports {\r\n    input:\r\n      input_bqsr_reports = BaseRecalibrator.recalibration_report,\r\n      output_report_filename = base_file_name + \".recal_data.csv\",\r\n      disk_size = flowcell_small_disk,\r\n      preemptible_tries = preemptible_tries\r\n  }\r\n...\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/epam/pipeline-builder/issues/comments/303092315","html_url":"https://github.com/epam/pipeline-builder/issues/15#issuecomment-303092315","issue_url":"https://api.github.com/repos/epam/pipeline-builder/issues/15","id":303092315,"user":{"login":"sidoruka","id":20998291,"avatar_url":"https://avatars1.githubusercontent.com/u/20998291?v=3","gravatar_id":"","url":"https://api.github.com/users/sidoruka","html_url":"https://github.com/sidoruka","followers_url":"https://api.github.com/users/sidoruka/followers","following_url":"https://api.github.com/users/sidoruka/following{/other_user}","gists_url":"https://api.github.com/users/sidoruka/gists{/gist_id}","starred_url":"https://api.github.com/users/sidoruka/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sidoruka/subscriptions","organizations_url":"https://api.github.com/users/sidoruka/orgs","repos_url":"https://api.github.com/users/sidoruka/repos","events_url":"https://api.github.com/users/sidoruka/events{/privacy}","received_events_url":"https://api.github.com/users/sidoruka/received_events","type":"User","site_admin":false},"created_at":"2017-05-22T12:57:37Z","updated_at":"2017-05-22T12:57:37Z","body":"@jsotobroad , seems that a redeploy of an application was in progress when you were testing. Should work fine now."}}
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