Addresses #129.

Detailed description of changes

We are switching to GRCh38, with the target Ensembl version being 111. STARfusion and Fusioncatcher outputs will not be Ensembl version 111 but will be reannotated to the target version for consistency with the rest of the pipeline. We will be using the reference sequence with decoys from NCBI. Because this reference genome includes the chr prefix for every sequence, the process FASTAREMOVEPREFIX was added to create a new fasta when running with GRCh38. Logic was also added to gunzip the fasta file before further processing. The STARFusion reference is updated to the latest GRCh38 plug-n-play reference. the metafusion_blocklist points to an lifted over version of the reference. The AGFusion container was updated to support the updated ensembl versions (< 112). More chromosomes were removed from the rRNA bed processing.

The metafusion reference generation scripts were updated. bin/final_generate_v75_gene_bed.R was changed to bin/generate_gene_bed.R and logic to handle Ensembl's new annotation of UTRs was added. in bin/make_gene_info_for_forte.R, gene_id is used as the gene's symbol for the cases in which gene_name is missing.

The fact that the fasta now had to be preprocessed (GUNZIP_FASTA and FASTAREMOVEPREFIX) forced some logic changes throughout the script. The fasta output was now a channel, and downstream logic was expecting a file object. For example, Channel.of([id:params.genome], fasta) was fine before when fasta == params.fasta, but errors out when fasta is a channel. It also made sense to update several of the modules to use input conventions such as tuple val(meta), path(fasta) instead of those such as path(fasta) because the output of GUNZIP_FASTA and FASTAREMOVEPREFIX contains a meta object, and we would otherwise have to repeatedly modify the channel for older versions of those modules. As a result, many of the changes will simply be updates to modules and small changes to how channels containing the references are input into the processes.

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 mskcc/forte 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 --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).