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As mentioned in nf-core/rnaseq#245, the `pipeline_report.{html,txt}` files get written with `new File` instead of `file` which leads to weird behavior and creating an `s3:/` folder locally if the output folder is on AWS S3: ``` Thu 27 Jun - 09:03 ~/code/nf-core/rnaseq origin ☊ olgabot/salmon-gencode ✔ 28☀ ll --tree s3: Permissions Size User Date Modified Git Name drwxr-xr-x - olgabot 11 Jun 10:26 -- s3: drwxr-xr-x - olgabot 11 Jun 10:26 -- └── olgabot-maca drwxr-xr-x - olgabot 11 Jun 10:26 -- └── mini-maca drwxr-xr-x - olgabot 11 Jun 10:26 -- └── results drwxr-xr-x - olgabot 11 Jun 10:26 -- └── pipeline_info .rw-r--r-- 12k olgabot 11 Jun 16:40 -- ├── pipeline_report.html .rw-r--r-- 2.7k olgabot 11 Jun 16:40 -- └── pipeline_report.txt ``` This is especially problematic as after the first time the pipeline is run, then the `s3:/` folder is created and any input files get tested against that "folder" and suddenly they "don't exist" because they look like they're on the local filesystem as locally, `s3://` --> `s3:/`, and then pipelines break 😢
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Requires a CHANGELOG update, other than that looking good 👍
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As mentioned in nf-core/rnaseq#245, the
pipeline_report.{html,txt}files get written withnew Fileinstead offilewhich leads to weird behavior and creating ans3:/folder locally if the output folder is on AWS S3:This is especially problematic as after the first time the pipeline is run, then the
s3:/folder is created and any input files get tested against that "folder" and suddenly they "don't exist" because they look like they're on the local filesystem as locally,s3://-->s3:/, and then pipelines break 😢Many thanks to contributing to nf-core/tools!
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docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/tools/tree/master/.github/CONTRIBUTING.md