Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS process

[drpatelh]

Description of feature

A number of users have been confused by the fact that it appears like RSEM is running as a result of this process RSEM_PREPAREREFERENCE_TRANSCRIPTS even though they aren't using the --aligner star_rsem option.

That process is actually just leveraging the rsem-prepare-reference command to generate the transcriptome from the GTF and the genome fasta which is why I called it RSEM_PREPAREREFERENCE_TRANSCRIPTS, as shown in the code below:

rnaseq/subworkflows/local/prepare_genome.nf

Line 116 in 646723c

ch_transcript_fasta = RSEM_PREPAREREFERENCE_TRANSCRIPTS ( ch_fasta, ch_filter_gtf ).transcript_fasta

The reason I chose rsem-prepare-reference is that we know that the transcriptome will be compatible with Salmon too and if there are any issues with the conversion then RSEM tends to fail at this step to allow the user to "fix" their annotations.

We should probably rename this process to MAKE_TRANSCRIPTOME in the next release to avoid this common misconception.

[drpatelh]

Will be fixed in #763