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Check broken links #358

Merged
merged 11 commits into from
Dec 5, 2019
Merged

Check broken links #358

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4548242
Try out how the broken links action works
FriederikeHanssen Dec 5, 2019
cedee86
Test
FriederikeHanssen Dec 5, 2019
86d2cd2
Fix link to portal.scilife
FriederikeHanssen Dec 5, 2019
ae54bf1
Fix link to rRNAdatabase
FriederikeHanssen Dec 5, 2019
ee6f02c
Change VAR uses
FriederikeHanssen Dec 5, 2019
548c22c
Remove .yml file
FriederikeHanssen Dec 5, 2019
d6c083e
Updated Changelog
FriederikeHanssen Dec 5, 2019
cdd1e72
Merge branch 'dev' into check_broken_links
FriederikeHanssen Dec 5, 2019
cb78bdd
Fix Changelog linting
FriederikeHanssen Dec 5, 2019
ef1c6f1
Fix Changelog linting
FriederikeHanssen Dec 5, 2019
d01a846
Fix Changelog linting
FriederikeHanssen Dec 5, 2019
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -8,7 +8,8 @@
* Add information about SILVA licensing when removing rRNA to `usage.md`
* Fixed ansi colours for pipeline summary, added summary logs of alignment results
* Fixes an issue where multiqc fails to run with `--skipbiotypeQC` option [#353](https://github.com/nf-core/rnaseq/issues/353)
* Fixes label name in fastQC process, Issue #345
* Fixes broken links [#357](https://github.com/nf-core/rnaseq/issues/357)
* Fixes label name in fastQC process, Issue [#345]

#### Updated Packages

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -66,7 +66,7 @@ The nf-core/rnaseq pipeline comes with documentation about the pipeline, found i

### Credits

These scripts were originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)).
These scripts were originally written for use at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)).

Many thanks to other who have helped out along the way too, including (but not limited to):
[@Galithil](https://github.com/Galithil),
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -445,7 +445,7 @@ flag (or set to true in your config file) to copy these files when complete.

### `--rRNA_database_manifest`

By default, rRNA databases in github [`biocore/sortmerna/rRNA_databases`](https://github.com/biocore/sortmerna/tree/master/rRNA_databases) are used. Here the path to a text file can be provided that contains paths to fasta files (one per line, no ' or " for file names) that will be used for database creation for SortMeRNA instead of the default ones. You can see an example in the directory `assets/rrna-default-dbs.txt`. Consequently, similar reads to these sequences will be removed.
By default, rRNA databases in github [`biocore/sortmerna/rRNA_databases`](https://github.com/biocore/sortmerna/tree/master/data/rRNA_databases) are used. Here the path to a text file can be provided that contains paths to fasta files (one per line, no ' or " for file names) that will be used for database creation for SortMeRNA instead of the default ones. You can see an example in the directory `assets/rrna-default-dbs.txt`. Consequently, similar reads to these sequences will be removed.
Be aware that commercial/non-academic entities require [`licensing for SILVA`](https://www.arb-silva.de/silva-license-information) with these default databases.

## Library Prep Presets
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