Reverting changes to a non-linted version and added the umitools modules.

Added the umitools workflow and integrated it into the smrnaseq workflow

Add additional documentation to use UMI tools as part of the pipeline.
Most of the documentation has been copied from nf-core/rnaseq.

The bam2fq module is neccessary to convert the deduplicated bam
files back into a fastq format to be fed into the existing
pipeline.

Added the umitools extract modules.config lines from nf-core/rnaseq
to this pipeline.

Added configurations for umi deduplication.

Initial comit of the umi dedup subworkflow. The workflow combines
already existing modules of the pipeline and nf-core module to
deduplicate the reads by mapping them to the species genome and
re-converting them to fastq after deduplication.

includes the optional umitools deduplication step after the read
QC.

Added additional configuration to change the output file name of
samtools sort.

Added the documentation detailing the output files of the UMI-tools
deduplication step.

After deduplication the reads that remained unaligned to the
provided reference genome are merged with the set of deduplicated
reads to enable the use of the full spectrum of reads, independent
of potential reference bias. This behaviour can be deactivated by
setting --umi_merge_unmapped false

Information on the new --umi_merge_unmapped command were added to
both the CHANGELOG, as well as the output markdown script.

Includes the nf-core cat module to replace the custom concatenation
module.

Implements the use of the nf-core cat module.

deletes the now unused conatenation module.