Queasy Serpent

⚠️ Breaking change!

In line with a standardisation change across all of nf-core, we have changed the main parameter name for supplying files to the pipeline.
In this release, please use --input instead of --reads.
The parameter still works in the same way as before.

Pipeline Updates

• Increased resources for fastqc process (#143)
• Raised Nextflow version requirement to 20.07.1
• Updated template to nf-core/tools 1.13.3
• Renamed --reads to --input
• Added new --maxins and --minins parameters to pass on to Bismark
• New --em_seq preset
  • Sets bismark_maxins = 1000, clip_r1 = 8, clip_r2 = 8, three_prime_clip_r1 = 8, three_prime_clip_r2 = 8
• New --publish_dir_mode parameter to customise results folder behaviour
• Fix bug on AWS for bismark_hisat known splice file (#177)
• Moved parameter documentation into new nextflow_schema.json file
  • This improves web documentation and enables nf-core launch functionality. See https://nf-co.re/launch?pipeline=methylseq
• Added a -profile test_full config for running the pipeline with a full-size test dataset
  • See the config file for details
  • This will be used for automated release tests on AWS, results browsable on the website

Software updates

• Python base 3.7.3 > 3.8.8
• markdown 3.1.1 > 3.3.4
• pymdown-extensions 6.0 > 8.1.1
• pygments 2.6.1 > 2.8.1
• pigz 2.3.4 > 2.6
• samtools 1.9 > 1.11
• TrimGalore! 0.6.5 > 0.6.6
• Bowtie2 2.3.5 > 2.4.2
• Hisat2 2.2.0 > 2.2.1
• Bismark 0.22.3 > 0.23.0
• Picard 2.22.2 > 2.25.1
• MethylDackel 0.5.0 > 0.5.2
• MultiQC 1.8 > 1.10