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