Update modules required for rnaseq pipeline

[drpatelh]

Udpdating modules required for the nf-core/rnaseq pipeline

• Fix memory options in hisat2/build module
• Bump Preseq version and added meta.yml to get lint tests passing
• Add ability to auto-detect --genomeSAindexNbases for smaller genomes in star/genomegenerate module

[drpatelh]

hisat2/build tests are expected to fail here because we have had to rename the test directory to hisat2/build_test to get pytest to work.

star/genomegenerate tests are failing because the SARS-CoV-2 GTF doesn't have specific fields. Not much I can do about that for now but I have added placeholders to use the human data. Error is below:

Command error:

  Fatal INPUT FILE error, no exon lines in the GTF file: genome.gtf
  Solution: check the formatting of the GTF file, it must contain some lines with exon in the 3rd column.
            Make sure the GTF file is unzipped.
            If exons are marked with a different word, use --sjdbGTFfeatureExon .

  Apr 15 21:29:14 ...... FATAL ERROR, exiting

[drpatelh]

Ready for review @JoseEspinosa @KevinMenden

[KevinMenden]

LGTM! 👍
Bit annoying that we need three different tools now in the STAR module but what can you do 🤷

[JoseEspinosa]

Nice!

[drpatelh]

Bit annoying that we need three different tools now in the STAR module but what can you do

Yup, but this will save alot of failures being reported for the rnaseq pipeline and others. Those additional tools should have quite a small storage footprint too. I will compare the size of the containers and post here

[drpatelh]

Yup, almost 4 times the size 😏 But still much smaller than some of those Java beasts!

8.9M	depot.galaxyproject.org-singularity-star-2.6.1d--0.img
37M	depot.galaxyproject.org-singularity-mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2-59cdd445419f14abac76b31dd0d71217994cbcc9-0.img

[KevinMenden]

Yeah that's still really small! 👍