Command line options¶
To get a quick overview of all available command line options, run
nextflow run maxemil/PhyloMagnet --help
Query options¶
Fastq input (--fastq
)¶
Provide one or several short read samples (with wildcards in double quotes) in
fastq format to PhyloMagnet. The files can be in gzip compressed form.
E.g. "fastq/*.fastq.gz"
.
BioProject list (--project_list
)¶
Provide a list of BioProject identifiers (e.g. PRJNA324704
) in a single
file, one ID per line.
BioProject run IDs (--is_runs
)¶
Boolean value that modifies the --project_list
option such that it expects
run IDs instead of Project IDs (e.g. SRR3656745
). Default is false
Database (--database
)¶
Choose if you would like to download the sra data from ncbi’s (ncbi
) or
ena’s (ena
) servers (depending on where you are, this might make a huge
speed difference). Default is ena
Reference options¶
EggNOG reference Ids (--reference_classes
)¶
A file with identifiers from the EggNOG database, e.g. COG0051
or
ENOG410XPEN
. One ID per line.
Archived reference packages (--reference_packages
)¶
A single path to one or several compressed references packages (see the utility
script make_reference_packages.sh
in the utils
folder) from a previous
PhyloMagnet run. Can contain wildcards if put in double quotes. e.g.
"my_rpkg/*.tgz"
Local reference sequences (--local_ref
)¶
A single path to one or several local fasta files containing orthologous groups
of proteins. the referece sequences should be annotated with their taxonomy ID
in the NCBI taxonomy (e.g. 562.NC_011750
as the sequence record’s header,
562
being the taxID).
Output options¶
Output queries (--queries_dir
)¶
Output directory for queries; assembled contigs, placement results and summary
tables/figures get saved here. Defaults to queries
.
Output references (--reference_dir
)¶
Output directory for references; fasta files, alignments, model files and trees
get saved here. Defaults to references
.
Run parameters¶
Phylogenetic method (--phylo_method
)¶
Phylogentic tool used for the reconstruction of the reference tree. Only used
for references from EggNOG and local files, not packages. Accepted values:
iqtree
, fasttree
, raxml
.
Alignment method (--align_method
)¶
Alignment tool used to compute reference alignments. Only used for references
from EggNOG and local files, not packages.
Accepted values: maftt-*
, prank
.
Taxonomic lineage (--lineage
)¶
the lineage(s) to report occurences for. Can be either a list of labels provided
by the user (e.g. Rickettsiales,Holosporales
), a taxonmic rank (e.g.
family
), or both (e.g. Rickettsia,family
)
No. of CPUs (--cpus
)¶
No. of CPUs to use. For more fine-grained uage of resources per process change
the file nextflow.config
.
Threshold for plotting taxonomic labels (--plot_threshold
)¶
Threshold for filtering low frequent taxon labels from summary plots. e.g. label would not get plotted when present in only 1 out of 4 trees for default value. Threshold is checked per sample. Default: 0.25, accepted values between o and 1
Threshold for including taxonomic labels (--aLWR_threshold
)¶
Threshold of accumulated likelihood weight ratio (aLWR, see gappa
’s
documentation) to include labels in the summary table. Default 0.8, accepted
values between o and 1
MEGAN VM options file (--megan_vmoptions
)¶
File with options that are passed on to the Java virtual machine running MEGAN. Most importantly, state here the amount of memory that is available, e.g. -Xmx16G for 16GB. By default the file is expected to be in the execution directory. Example file MEGAN.vmoptions is included in the repository.
Location of MEGAN (--megan_dir
)¶
The directory MEGAN’s source files are located. When Manually installing MEGAN it could be something like /usr/local/megan. Leave as default if the singularity image is used.
Location of Python3 (--python3
)¶
Location of the python3 executable that has all needed packages available. Should usually be /usr/bin/env python3, leave as default is using the singularity image.