Example Usage

You can use PhyloMagnet in a number of different scenarios:

Using Bioproject IDs and eggNOG references

nextflow run maxemil/PhyloMagnet --reference_classes eggnog.txt \
                      --project_list bioprojects.txt \
                      --phylo_method fasttree \
                      --queries_dir queries_output \
                      --reference_dir ref_output \
                      --lineage Rickettsiales,family \
                      --megan_vmoptions MEGAN.vmoptions \
                      --cpus 20

Using SRA run IDs and local references

nextflow run maxemil/PhyloMagnet --local_ref customOG.fasta \
                      --project_list sra_runs.txt \
                      --is_runs true \
                      --phylo_method fasttree \
                      --queries_dir queries_output \
                      --reference_dir ref_output \
                      --lineage Rickettsiales,family \
                      --megan_vmoptions MEGAN.vmoptions \
                      --cpus 20

Using local FastQ file and local + eggNOG references

nextflow run maxemil/PhyloMagnet --reference_classes eggnog.txt \
                      --local_ref customOG.fasta \
                      --phylo_method fasttree \
                      --fastq local_metagenome.fastq.gz
                      --queries_dir queries_output \
                      --reference_dir ref_output \
                      --lineage Rickettsiales,family \
                      --megan_vmoptions MEGAN.vmoptions \
                      --cpus 20