v2.0 Release Candidate

[chris-cheshire]

Major Changes

• [#53] - Complete redesign of the samplesheet input system. Controls are no longer hard-coded to igg and the process of assigning controls to samples has been simplified.
• [#93], [#73] - Additional sample normalisation options have been added. In addition to normalising using detected spike-in DNA, there are now several options for normalising against read depth instead as well as skipping normalisation entirely.
• [#62] - Added MACS2 as an optional peak caller. Peak calling can now be altered using the peakcaller variable. Both peak callers can be run using --peakcaller SEACR,MACS2, the primary caller is the first item in the list and will be used downstream while the secondary will be run and outputted to the results folder.
• [#101] - v1.1 ran consensus peak calling at both the group level and for all samples. This was causing performance issues for larger sample sets. There is now a new consensus_peak_mode parameter that defaults to group. Consensus will only be run on all samples if this is changed to all.

Enhancements

• Updated pipeline template to nf-core/tools 2.3.2.
• Upgraded pipeline to support the new nf-core module configuration system.
• More robust CI testing. Over 213 tests now before any code is merged with the main code base.
• More control over which parts of the pipeline run. Explicit skipping has been implemented for every section of the pipeline.
• Added options for scaling control data before it is used to call peaks. This is especially useful when using read depth normalisation as this can sometimes result in few peaks being called due to high background levels.
• Added support for Bowtie2 large indexes.
• IGV auto-session builder now supports gff and fna file extensions.
• Bowtie2 alignment has been altered to run in --end-to-end mode only if trimming is skipped. If trimming is activated then it will run in --local mode.
• [#88] - Many processes have been optimized for resource utilization. Users will especially notice that single thread processes will now only request 1 core rather than 2.
• [#63] - Custom containers for python reporting have now been condensed into a single container and added to BioConda.
• [#76] - Standardized python versions across reporting modules.

Fixes

• [#120] - DeepTools compute matrix/heatmaps now only runs if there are peaks detected.
• [#99] - Large upset plots were causing process crashes. Upset plots will now fail gracefully if the number of samples in the consensus group is more than 10.
• [#95] - Fixed FRIP calculation performance issues and crashes.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
samtools	1.14	1.15.1
bowtie2	2.4.2	2.4.4
picard	2.25.7	2.27.1

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/cutandrun branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[FriederikeHanssen]

Love it, just some teeny tiny things from my side mostly about version and test data.