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@ewels ewels released this 26 Mar 16:07
· 953 commits to master since this release
1.6
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⚠️ 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
  • 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
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