Update the pipeline to address reviewers comments [ci skip] (#10)
* Reinitialize pipeline with nf-core template [ci skip]
* install relevant modules [ci skip]
* add the fully concatenated file [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* download assemblies using ncbi-datasets-cli [ci skip]
* add more references for reviewer-assemblies [ci skip]
* add download script [ci skip]
* dev iteration [ci skip]
* use baseline java8 for orthoani [ci skip]
* add orthoani util modules [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* update the hardware req for trimmomatic [ci skip]
* add ggdc results [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* restore spades in favor of util process for filtering [ci skip]
* add post-spades utils [ci skip]
* add post-spades utils [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* make fastgrep executable [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* test with latest checkm process [ci skip]
* retry with 1.1.8 checkm and reduced tree [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* dev iteration [ci skip]
* regenrate the ggdc results [ci skip]
* add params and orthoani subworkflow [ci skip]
* use a custom container [ci skip]
* use lower resources [ci skip]
* add raxml [ci skip]
* add raxml [ci skip]
* add raxml [ci skip]
* add raxml [ci skip]
* add raxml [ci skip]
* add orthofinder [ci skip]
* add orthofinder [ci skip]
* add orthofinder [ci skip]
* add orthofinder [ci skip]
* iterate on orthofinder [ci skip]
* iterate on orthofinder [ci skip]
* iterate on orthofinder [ci skip]
* iterate on orthofinder [ci skip]
* iterate on orthoani [ci skip]
