Merge branch 'dev' into sex-det-collision

Author: jfy133

CHANGELOG.md

@@ -7,26 +7,29 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-- [#676](https://github.com/nf-core/eager/issues/676) - Added Lib Checks and automatic help message / summary message formatting
+- [#676](https://github.com/nf-core/eager/issues/676) - Refactor help message / summary message formatting to automatic versions using nf-core library
+- [#682](https://github.com/nf-core/eager/issues/682) - Add AdapterRemoval `--qualitymax` flag to allow FASTQ Phred score range max more than 41
 
 ### `Fixed`
 
 - [#666](https://github.com/nf-core/eager/issues/666) - Fixed input file staging for `print_nuclear_contamination`
 - [#631](https://github.com/nf-core/eager/issues/631) - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
 - Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
-- [#652](https://github.com/nf-core/eager/issues/652) Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
+- [#652](https://github.com/nf-core/eager/issues/652) - Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
 - [#626](https://github.com/nf-core/eager/issues/626) - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty
 - Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
-- [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file
+- [#673](https://github.com/nf-core/eager/pull/673) - Fix Kraken database loading when loading from directory instead of compressed file
 - [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
 - [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex
 - Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails
 - [#672](https://github.com/nf-core/eager/issues/672) - Removed java parameter from picard tools which could cause memory issues
 - [#679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
 - [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case
 - [#693](https://github.com/nf-core/eager/issues/693) - Fixed broken TSV input validation for the Colour Chemistry column
+- [#695](https://github.com/nf-core/eager/issues/695) - Fixed incorrect `-profile` order in tutorials (originally written reversed due to [nextflow bug](https://github.com/nextflow-io/nextflow/issues/1792))
 - [#653](https://github.com/nf-core/eager/issues/653) - Fixed file collision errors with sexdeterrmine for two same-named libraries with different strandedness
 
+
 ### `Dependencies`
 
 - Bumped MultiQC to 1.10 for improved functionality

README.md

@@ -158,6 +158,7 @@ of this pipeline:
 
 Those who have provided conceptual guidance, suggestions, bug reports etc.
 
+* [Alexandre Gilardet](https://github.com/alexandregilardet)
 * Arielle Munters
 * [Charles Plessy](https://github.com/charles-plessy)
 * [Åshild Vågene](https://github.com/ashildv)