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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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apeltzer
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Jul 3, 2019
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apeltzer
approved these changes
Jul 3, 2019
| @@ -49,7 +49,7 @@ def helpMessage() { | |||
| * SET UP CONFIGURATION VARIABLES | |||
| */ | |||
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| // Show help message | |||
| // Show help emssage | |||
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| // Show help emssage | |
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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!
Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
PR checklist
docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/tools/tree/master/.github/CONTRIBUTING.md