Patch 1.3.1

[tkchafin]

• Fix for HiC CRAM inputs since 1.1.0
• For for PacBio FASTQ inputs since 1.3.0
• Correct the license

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
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• 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).

[tkchafin]

Not sure what the EditorConfig fail is

[tkchafin]

editorconfig-checker is passing locally

[tkchafin]

editorconfig-checker is some issue introduced in the latest update, fixing to prior version resolves the issue. I think should be ready to review now.

[reichan1998]

Looks great, thank you! It's working well.

[muffato]

• In this pipeline we also keep track of the citations in CITATIONS.md. Can you add bbtools there ?