nf-core/eager: [2.3.2] - Aalen (Patch) - 2021-01-14

Added

• #687 - Adds Kraken2 unique kmer counting report
• #676 - Refactor help message / summary message formatting to automatic versions using nf-core library
• #682 - Add AdapterRemoval --qualitymax flag to allow FASTQ Phred score range max more than 41

• #666 - Fixed input file staging for print_nuclear_contamination
• #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 - Added note to documentation that when using --skip_collapse this will use paired-end alignment mode with mappers when using PE data
• #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 - Fix Kraken database loading when loading from directory instead of compressed file
• #688 - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
• #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 - Removed java parameter from picard tools which could cause memory issues
• #679 - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
• #690 - Fixed ANGSD output mode for beagle by setting -doMajorMinor 1 as default in that case
• #693 - Fixed broken TSV input validation for the Colour Chemistry column
• #695 - Fixed incorrect -profile order in tutorials (originally written reversed due to nextflow bug)
• #653 - Fixed file collision errors with sexdeterrmine for two same-named libraries with different strandedness

• Bumped MultiQC to 1.10 for improved functionality
• Bumped HOPS to 0.35 for MultiQC 1.10 compatibility