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Added troubleshooting pipeline updating
Due to currently not being able to combine paired/single end data.
This information is only useful for admins/installer of software not user.
Also removed reference to assembly projects - the poly-G isn't a true complexity filter.
Documentation improvements
Improve pipeline tests
Bam support
Made more specific --bwa_index is path to dir
Rename reference to fasta in all cases
Version 2.0.5 PR for release
Bump environment versions
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See changelog for full details differences between 2.0.4 and 2.0.5!
PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md