Address #596

Author: jfy133

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#591](https://github.com/nf-core/eager/issues/591) - Fixed offset underlines in lane merging diagram in docs
 - [#592](https://github.com/nf-core/eager/issues/592) - Fixed issue where supplying Bowtie2 index reported missing bwamem_index error
 - [#590](https://github.com/nf-core/eager/issues/592) - Removed redundant dockstore.yml from root
+- [#596](https://github.com/nf-core/eager/issues/596) - Add workaround for issue regarding gzipped FASTAs and pre-built indices
 
 ## [2.2.0] - Ulm - 2020-10-20
 

docs/usage.md

@@ -735,6 +735,10 @@ If you want to use pre-existing `bwa index` indices, please supply the
 nf-core/eager will automagically detect the index files by searching for the
 FASTA filename with the corresponding `bwa` index file suffixes.
 
+> :warning: pre-built indices must currently be built on non-gzipped FASTA files
+> due to limitations of `samtools`. However once indices have been built, you
+> can re-gzip the FASTA file as nf-core will unzip this particular file for you.
+
 For example:
 
 ```bash
@@ -756,6 +760,10 @@ If you want to use pre-existing `bt2 index` indices, please supply the
 nf-core/eager will automagically detect the index files by searching for the
 FASTA filename with the corresponding `bt2` index file suffixes.
 
+> :warning: pre-built indices must currently be built on non-gzipped FASTA files
+> due to limitations of `samtools`. However once indices have been built, you
+> can re-gzip the FASTA file as nf-core will unzip this particular file for you.
+
 For example:
 
 ```bash
@@ -789,6 +797,10 @@ If you want to use a pre-existing `picard CreateSequenceDictionary` dictionary
 file, use this to specify the required `.dict` file for the selected reference
 genome.
 
+> :warning: pre-built indices must currently be built on non-gzipped FASTA files
+> due to limitations of `samtools`. However once indices have been built, you
+> can re-gzip the FASTA file as nf-core will unzip this particular file for you.
+
 For example:
 
 ```bash