ARTR-seq Streamlined Version

[hanzhong-bai]

Description

The ARTR_seq_streamline branch added a feature of running whole-read CLIP-seq/ARTR-seq analysis and calls peaks using MACS3. These include:

1. A new "PARSE_PAIRWISE_INPUT" subworkflow parsing the add-on pairwise samplesheet
2. A "PREP_WHOLE_READ" subworkflow processing dedupped reads for peak calling and bigwig visualisations in IGV
3. A "rearrangeChannels" function and workflow overhaul resolving pairwise calling using MACS3
4. Inclusion of "crick.config" profile allowing for pipeline running on NEMO at crick

Everything is under the control of the "whole_read_analysis" boolean parameter, which, when set true, deactivates crosslink preparation, crosslink peak calling and subsequent analyses.

The pipeline requires an additional input samplesheet denoting the pairwise relationships for MACS3 calling, and currently only supports read 1 input. The output files include MACS3 output and bigwig files for visualisation in IGV.

How Has This Been Tested?

1. nf-test modular testing of subworkflows (tests/subworkflows/local)
2. nextflow profile testing (conf/test_artr_seq.config)
3. Mock run on HeLa cell ARTR-seq samples (tests/ARTR-seq/script/ARTR-seq-test.sh [private])

All tests finished without errors or warnings.

Things Remaining To Be Done/Things I Couldn't Do:

• Schema update (couldn't run 'nf-core schema build' for some reason)
• Linting ('nf-core lint' required too many changes)
• Docs update