Update pipeline to regenerate the results as per reviewers comments
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]