Use file instead of new File
#245
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As I learned [here](nextflow-io/nextflow#1185), `file` != `new File` and `new File` doesn't know how to handle S3 paths. This leads to weird behavior like creating an `s3:` folder, with all the bucket "subfolders" when a pipeline is run: ``` 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 ```
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(I'm testing out this edit here before editing nf-core/tools) |
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Oh, good spot! Please test and then ping someone for reviewing! (and add it upstream in tools, yes! ) |
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Okay (I think) this is ready for review! |
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Jul 3, 2019
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 😢
This was referenced Jul 3, 2019
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As I learned here,
file!=new Fileandnew Filedoesn't know how to handle S3 paths. This leads to weird behavior like creating ans3:folder, with all the bucket "subfolders" when a pipeline is run:PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md