Add 2FAST2Q as an alternative to the MAGeCK count / Bowtie2 combo on the screening workflow

Description of feature

Hi,

I think it would be interesting to offer an alternative to the current MAGeCK count or Bowtie2 approach (step2 on the screening workflow).

Let me introduce to you 2FAST2Q. By integrating this tool, available now also as a nf-core module (https://nf-co.re/modules/fast2q/), we would expand the current pipeline to the following:

1. Accept reads with mutiple features (such as 2 or more sgRNAs per read), and count these events.
2. Have the possibility of directly searching for features when these are delimited by any given up/downstream sequences. Expanding on this, have the possibility of directly pulling and counting any new found sequences without the need for a library file (optional).
3. Directly configure and filter based on sequence alignment mismatches (Hamming distance only), and sequence phred-scores.

2FAST2Q would essentialy sit as a read count matrix file provider.

Some considerations would be:

1. The output is in raw read counts (unnormalized). CRISPRseq´s following steps require normalized read counts.
2. The output displays only sgRNA names and respective counts (rows) per fastq file (columns). CRISPRseq´s current count matrix file includes sgRNA names AND respective linked genes.

I would be happy to work on this if this is a proposition you agree with.

Start by reviewing step 2 of the screening workflow and the linked nf-core 2FAST2Q module. Define how the alternative would provide raw counts while fitting downstream normalization and gene-linking requirements; the issue names no repository files or tests to run.