Update fastq file inputs, enforce gzipp-ed inputs

[skchronicles]

About

The pipeline currently accepts BAM fand fastq files as input. At the current moment, it expects that the fastq file are not gzipp-ed. To reduce disk space, let's enforce that the input fastq files are gzipped or compressed, i.e. fastq.gz extension. All the current assembler we are using work with compressed fastq files as input: Raven, Flye, and Hifiasm. As so, it makes sense to use compressed files as input.

At the current moment, there is also a bug where if you do provide a compressed fastq file as input, i.e. fastq.gz extension. It retries to create a renamed symlink (which doesn't work) and it errors out with a message stating how to incorrectly fix the problem. That needs to be addressed too.

[skchronicles]

The input fastq files do not need to be converted to fasta format. Remove any conversions for input fastq files. We do need to convert input BAM files to fasta format. Flye does not work with BAM files. So we only really need to convert to fasta files for bam files.