Merge pull request #55 from luslab/dev

R_sessionInfo.log

dev/docker/static_reports/test_data/*

dev/docker/static_reports/test_output/*

!dev/docker/static_reports/test_data/_dummy.txt

!dev/docker/static_reports/test_output/_dummy.txt

!tests/data/

.vscode/

profile.svg

We thank Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and everyone in the Luscombe Lab ([@luslab](https://github.com/luslab)) for their extensive assistance in the development of this pipeline.

![[The Francis Crick Institute](https://www.crick.ac.uk/)](docs/images/crick_logo.png)

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).

        - It can be due to the Tn5 preference.

        - What you might be detecting is the 10-bp periodicity that shows up as a sawtooth pattern in the length distribution. If so, this is normal and will not affect alignment or peak calling. In any case we do not recommend trimming as the bowtie2 parameters that we list will give accurate mapping information without trimming.

# fastqc_config:

#     fastqc_theoretical_gc: "hg38_genome"

# extra_fn_clean_exts:

#   - ".spikein.bowtie2"

#   - "_processedFile"

# extra_fn_clean_trim:

#   - "#"

#   - ".myext"

# Customise the module search patterns to speed up execution time

#  - Skip module sub-tools that we are not interested in

#  - Replace file-content searching with filename pattern searching

#  - Don't add anything that is the same as the MultiQC default

# See https://multiqc.info/docs/#optimise-file-search-patterns for details

sp:

    cutadapt:

        fn: '*trimming_report.txt'