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Fix the test-sample-sheet tests/csv/3.0/mapped_joint_bam.csv #872

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asp8200 opened this issue Nov 28, 2022 · 0 comments
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Fix the test-sample-sheet tests/csv/3.0/mapped_joint_bam.csv #872

asp8200 opened this issue Nov 28, 2022 · 0 comments
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asp8200 commented Nov 28, 2022

Description of the bug

https://nfcore.slack.com/archives/C02MDBZAYJK/p1669641933059249

Change the content of the patient- and sample-fields in tests/csv/3.0/mapped_joint_bam.csvso that they correspond to the ids in the bam-files, that is, test -> testN and test1 -> testT:

patient,status,sample,bam,bai
testN,0,testN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai
testT,0,testT,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai

This change will probably also require that some md5sums in tests/test_haplotypecaller.yml are updated.

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@asp8200 asp8200 added the bug Something isn't working label Nov 28, 2022
@asp8200 asp8200 self-assigned this Nov 28, 2022
@asp8200 asp8200 removed the bug Something isn't working label Nov 28, 2022
asp8200 added a commit to asp8200/sarek that referenced this issue Dec 5, 2022
@asp8200 asp8200 mentioned this issue Dec 6, 2022
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