Merge pull request #358 from FriederikeHanssen/check_broken_links

Check broken links

CHANGELOG.md

@@ -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
 

README.md

@@ -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),

docs/usage.md

@@ -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