[Do not merge!] Pseudo PR for first release #9
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Added a 'target' parameter
Keeping it causes the pipeline to crash because of our changes in assets/schema_input.json.
Run assembly scan
These includes seed, skip_dotplot___, targerName
Added 1st batch of new parameters
to overide the default target parameter, which is null and now target
Im waiting for your input concerning whether or not to use the 'if' here or nort to accomodate m2m, o2m, ...
Im waiting for your input concerning whether or not to use the 'if' here or nort to accomodate m2m, o2m, ...
val(format)
Running more modules
Let's discuss this over on slack. But you can maybe see how that is done using the following example https://github.com/MultiQC/test-data/blob/main/data/custom_content/embedded_config/table_headers_mqc.txt |
Co-authored-by: Matthias Hörtenhuber <[email protected]>
This reverts commit 3e349a9.
Also remove old tube map file
Updated the logo/map
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Hi @mashehu I think that we addressed all of your comments. The MultiQC report would benefit from more polishing but maybe that can be deferred to a later release? One final thing that I could not fix is that on the https://nf-co.re/pairgenomealign/dev/ page the pipeline's workflow image does not display, despite that it does fine on GitHub… |
| ### FastQC | ||
| Each _query_ genome, is aligned to the _target_ genome, and each alignment is visualised with dot plots. The output file names are constructed by concatenating the _target_ and _query_ sample identifiers with a `___` separator (three underscores), to faciliate re-extraction of the IDs from file names. | ||
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| ### Assembly statistics |
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| ### Assembly statistics | |
| ## Assembly statistics |
If you decrease the heading level of this and the following headings to h2, the will show up in the ToC on the side. 🙂
| @@ -72,7 +72,11 @@ For more details about the output files and reports, please refer to the | |||
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| We thank the following people for their extensive assistance in the development of this pipeline: | |||
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| - [Mahdi Mohammed](https://github.com/U13bs1125): ported the original pipeline to _nf-core_ template 2.14.x. | |||
| - [Mahdi Mohammed](https://github.com/U13bs1125) ported the original pipeline to _nf-core_ template 2.14.x. | |||
| - [Martin Frith](https://github.com/mcfrith/), the author of LAST, gave us extensive feedback and advices. | |||
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| - [Martin Frith](https://github.com/mcfrith/), the author of LAST, gave us extensive feedback and advices. | |
| - [Martin Frith](https://github.com/mcfrith/), the author of LAST, gave us extensive feedback and advice. |
| id: | ||
| title: "ID" | ||
| description: "target___query" |
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Not sure why this is not working, but not such a big thing maybe...
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Closing as 1.0.0 is out 🎉 |
Do not merge! This is a PR of dev compared to the TEMPLATE branch for whole-pipeline reviewing purposes. Changes should be made to dev and this PR should not be merged into first-commit-for-pseudo-pr!