{"action":"closed","issue":{"url":"https://api.github.com/repos/nf-core/eager/issues/219","repository_url":"https://api.github.com/repos/nf-core/eager","labels_url":"https://api.github.com/repos/nf-core/eager/issues/219/labels{/name}","comments_url":"https://api.github.com/repos/nf-core/eager/issues/219/comments","events_url":"https://api.github.com/repos/nf-core/eager/issues/219/events","html_url":"https://github.com/nf-core/eager/issues/219","id":453713375,"node_id":"MDU6SXNzdWU0NTM3MTMzNzU=","number":219,"title":"Supplying a bwa index produces only single sample output for mapping","user":{"login":"ktmeaton","id":14981272,"node_id":"MDQ6VXNlcjE0OTgxMjcy","avatar_url":"https://avatars0.githubusercontent.com/u/14981272?v=4","gravatar_id":"","url":"https://api.github.com/users/ktmeaton","html_url":"https://github.com/ktmeaton","followers_url":"https://api.github.com/users/ktmeaton/followers","following_url":"https://api.github.com/users/ktmeaton/following{/other_user}","gists_url":"https://api.github.com/users/ktmeaton/gists{/gist_id}","starred_url":"https://api.github.com/users/ktmeaton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ktmeaton/subscriptions","organizations_url":"https://api.github.com/users/ktmeaton/orgs","repos_url":"https://api.github.com/users/ktmeaton/repos","events_url":"https://api.github.com/users/ktmeaton/events{/privacy}","received_events_url":"https://api.github.com/users/ktmeaton/received_events","type":"User","site_admin":false},"labels":[{"id":953157741,"node_id":"MDU6TGFiZWw5NTMxNTc3NDE=","url":"https://api.github.com/repos/nf-core/eager/labels/bug","name":"bug","color":"d73a4a","default":true},{"id":953157751,"node_id":"MDU6TGFiZWw5NTMxNTc3NTE=","url":"https://api.github.com/repos/nf-core/eager/labels/good%20first%20issue","name":"good first issue","color":"7057ff","default":true}],"state":"closed","locked":false,"assignee":{"login":"apeltzer","id":2359510,"node_id":"MDQ6VXNlcjIzNTk1MTA=","avatar_url":"https://avatars3.githubusercontent.com/u/2359510?v=4","gravatar_id":"","url":"https://api.github.com/users/apeltzer","html_url":"https://github.com/apeltzer","followers_url":"https://api.github.com/users/apeltzer/followers","following_url":"https://api.github.com/users/apeltzer/following{/other_user}","gists_url":"https://api.github.com/users/apeltzer/gists{/gist_id}","starred_url":"https://api.github.com/users/apeltzer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apeltzer/subscriptions","organizations_url":"https://api.github.com/users/apeltzer/orgs","repos_url":"https://api.github.com/users/apeltzer/repos","events_url":"https://api.github.com/users/apeltzer/events{/privacy}","received_events_url":"https://api.github.com/users/apeltzer/received_events","type":"User","site_admin":false},"assignees":[{"login":"apeltzer","id":2359510,"node_id":"MDQ6VXNlcjIzNTk1MTA=","avatar_url":"https://avatars3.githubusercontent.com/u/2359510?v=4","gravatar_id":"","url":"https://api.github.com/users/apeltzer","html_url":"https://github.com/apeltzer","followers_url":"https://api.github.com/users/apeltzer/followers","following_url":"https://api.github.com/users/apeltzer/following{/other_user}","gists_url":"https://api.github.com/users/apeltzer/gists{/gist_id}","starred_url":"https://api.github.com/users/apeltzer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apeltzer/subscriptions","organizations_url":"https://api.github.com/users/apeltzer/orgs","repos_url":"https://api.github.com/users/apeltzer/repos","events_url":"https://api.github.com/users/apeltzer/events{/privacy}","received_events_url":"https://api.github.com/users/apeltzer/received_events","type":"User","site_admin":false}],"milestone":null,"comments":4,"created_at":"2019-06-07T22:17:06Z","updated_at":"2019-06-09T09:46:39Z","closed_at":"2019-06-09T09:46:39Z","author_association":"NONE","body":"**Describe the bug**\r\nHi EAGER team, the -r dev branch appears to have strange behavior when supplying a bwa index. Multi-sample runs behave as expected through trimming and merging but for mapping and downstream tools only one sample is processed before it finishes. I haven't been able to figure this out so if you have this resolved this or if it's a misunderstanding of usage on my part that would be great to know!\r\n\r\nIn this example, there are 3 paired-end libraries TestData01, TestData02, and TestData03. Only TestData02 runs through bwa and subsequent steps.\r\n\r\n[warm up] executor > local\r\n[3d/68dca2] Submitted process > makeSeqDict (Enterobacteria_phage_lambda.fasta)\r\n[e1/fd8ece] Submitted process > fastqc (TestData01)\r\n[15/f40e74] Submitted process > fastqc (TestData02)\r\n[cd/de2157] Submitted process > fastqc (TestData03)\r\n[95/cf6b08] Submitted process > adapter_removal (TestData02)\r\n[d5/0e17b6] Submitted process > adapter_removal (TestData03)\r\n[af/5e7530] Submitted process > adapter_removal (TestData01)\r\n[2f/cb712f] Submitted process > output_documentation\r\n[71/60e771] Submitted process > fastqc_after_clipping (TestData02.pass_1.fastq)\r\n[ed/b567d4] Submitted process > bwa (TestData02.pass_1.fastq)\r\n[8e/be6de0] Submitted process > fastqc_after_clipping (TestData03.pass_1.fastq)\r\n[66/dcb279] Submitted process > fastqc_after_clipping (TestData01.pass_1.fastq)\r\n[cb/d83538] Submitted process > samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)\r\n[85/7f3264] Submitted process > damageprofiler (TestData02.pass_1.fastq.combined.fq.sorted)\r\n[a1/61e362] Submitted process > samtools_filter (TestData02.pass_1.fastq.combined.fq.sorted.bam)\r\n[8b/109241] Submitted process > qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)\r\n[55/6b513b] Submitted process > dedup (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)\r\n[8b/c327d5] Submitted process > get_software_versions (1)\r\n[e9/38c8dd] Submitted process > preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)\r\n[15/2bc362] Submitted process > multiqc\r\nWarning, pipeline completed, but with errored process(es)\r\nNumber of ignored errored process(es) : 0 \r\nNumber of successfully ran process(es) : 20 \r\n[nf-core/eager]Pipeline completed successfully\r\n\r\n**To Reproduce**\r\nSteps to make me able to reproduce the behavior:\r\n1. The pipeline command causing the problematic behavior is included in the file:  [command_test_devIndex.txt](https://github.com/nf-core/eager/files/3267759/command_test_devIndex.txt)\r\n2. Functionality can be rescued by either removing the parameter --bwa_index, or by running the pipeline with the -r master branch and then resetting the --bwa_index to the reference directory.\r\n\r\n**Expected behavior**\r\nIn the test case, I would expect the remaining three files (TestData01 and TestData03) to also complete mapping, qualimap, dedup, etc.) since this is what happens in the master branch or without a bwa index supplied.\r\n\r\n**Operating System:**\r\n - OS: CentOS 6.10\r\n - nf-core/eager revision: 59fbcc1007 [dev]\r\n\r\n**Additional Files**\r\n[devIndex.nextflow.log](https://github.com/nf-core/eager/files/3267777/devIndex.nextflow.log)\r\n\r\nThank you!\r\n\r\n"}}
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