Update README according to https://github.com/nf-core/tools/issues/2186 #946
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@nf-core-bot fix linting |
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jfy133
approved these changes
Feb 20, 2023
grst
commented
Feb 20, 2023
Co-authored-by: James A. Fellows Yates <[email protected]>
drpatelh
reviewed
Mar 10, 2023
| You can find numerous talks on the [nf-core events page](https://nf-co.re/events) from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out! | ||
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| ## Pipeline summary | ||
| **nf-core/rnaseq** is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report. | ||
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Suggested change
| ## Tube map | |
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I wouldn't call it Tube map, 'Workflow Diagram' or something would be better
drpatelh
reviewed
Mar 10, 2023
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| > **Note** | ||
| > The SRA download functionality has been removed from the pipeline (`>=3.2`) and ported to an independent workflow called [nf-core/fetchngs](https://nf-co.re/fetchngs). You can provide `--nf_core_pipeline rnaseq` when running nf-core/fetchngs to download and auto-create a samplesheet containing publicly available samples that can be accepted directly as input by this pipeline. | ||
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| 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html)) |
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Suggested change
| 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html)) | |
| ## Pipeline overview | |
| 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html)) |
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Added a couple of sections because everything looks bunched up otherwise.
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I'm not sure we need a section both above and below the tube map... the tube map would fit well under both "introduction" and "pipeline overview"
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I agree with Gregor, going that route for the template update for the moment. Feel frre to reject the PR, @drpatelh :D
drpatelh
reviewed
Mar 10, 2023
drpatelh
reviewed
Mar 10, 2023
drpatelh
reviewed
Mar 10, 2023
drpatelh
reviewed
Mar 10, 2023
drpatelh
requested changes
Mar 10, 2023
Co-authored-by: Harshil Patel <[email protected]>
Co-authored-by: Harshil Patel <[email protected]>
grst
commented
Mar 10, 2023
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| > **Note** | ||
| > The SRA download functionality has been removed from the pipeline (`>=3.2`) and ported to an independent workflow called [nf-core/fetchngs](https://nf-co.re/fetchngs). You can provide `--nf_core_pipeline rnaseq` when running nf-core/fetchngs to download and auto-create a samplesheet containing publicly available samples that can be accepted directly as input by this pipeline. | ||
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| 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html)) |
There was a problem hiding this comment.
I'm not sure we need a section both above and below the tube map... the tube map would fit well under both "introduction" and "pipeline overview"
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Are we still waiting on other things being added for this to be merged @grst @FriederikeHanssen ? |
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Two links are still pointing to non-existing pages on the website. |
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Yep what will be removed needs to be added to the website somewhere: https://nfcore.slack.com/archives/C01QPMKBYNR/p1678782050033109 |
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Ok, this may have to wait until the next release then which shouldn't be too long after the Hackathon. Want to get a release out in the next couple of days. |
grst
commented
Mar 23, 2023
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@nf-core-bot fix linting |
drpatelh
approved these changes
Mar 23, 2023
Merged
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PR checklist
[ ] If you've fixed a bug or added code that should be tested, add tests![ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.nf-core lint)- [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).- [ ] Usage Documentation indocs/usage.mdis updated.- [ ] Output Documentation indocs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).