04. Parameters

A typical pipesnake command might look like this:

nextflow run ausarg/pipesnake --input samplesheet.csv --outdir <OUTDIR> -profile docker

But there are many parameters we can change to fit the workflow to our needs. We outline all available parameters in the parameters-usage file, but below we highlight a limited number that are most likely to be of broad interest.

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Required pipesnake Parameters

Required Parameter	Type	Description
--input	string	Path to comma-separated file containing information about the samples in the experiment.
--outdir	string	The output directory where the results will be saved. You must use absolute paths to storage on Cloud infrastructure.
--blat_db	string	Path to the target sequences FASTA file.

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Optional pipesnake Parameters

Optional Parameter	Type	Description
--filter	string	Path to the filter sequences FASTA file. Only if --disable_filter false.
--tree_method	string	Default is iqtree. The supported options are: iqtree or raxml. Both methods should offer qualitatively identical results.
--assembly	string	Default is trinity. Supported software options for contig assembly are: trinity or SPAdes. SPAdes is generally considerably faster, but results should be comparable. Trinity is retained for consistency with existing phylogenomic projects.
--trim_alignment	boolean	Default is true. Trim initial MAFFT alignments using GBLOCKS. If true there are a number of additional GBLOCKS parameters that can be optimized.
--batching_size	integer	Default is 250. Number of alignment files to be processed sequentially in batches to avoid submitting a large number of jobs when using HPCs.
--trinity_scratch_tmp	boolean	Default is true. Trinity generates large number of intermediate files. This can be an issue for some HPCs that limits the file number for each user. This option will make trinity writes to the /tmp directory on the compute node then copy the compressed output directory (not the fasta) to the working directory to avoid this issue.
--phylogeny_make_alignments_minsamp	integer	Default is 4 Minimum number of samples to constitute an alignment Some phylogeny building methods rely on a minimum number of samples in an alignment. E.g. to estimate bootstraps for a genetree (IQTREE/RAxML) or include a genetree in an ASTRAL analysis, the minimum number of samples is 4.
--make_rgb_kept_tags	string	Default is easy_recip_match,complicated_recip_match easy_recip_match: 1-to-1 unique match between contig and targeted locus complicated_recip_match: 1-to-1 non-unique match, in which one targeted locus matches to multiple contigs if you'd like a stricter search (fewer, more-reliable matches) use --make_rgb_kept_tags easy_recip_match only.
--stage	string	Default is from-start from-start: runs pipeline from raw data (fastq.gz) through to end from-prg: runs pipeline from PRGs through to end For more info about running the pipeline from the start or the middle, see here

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Optional Nextflow Parameters

Optional Parameter	Type	Description
-resume	string	Will resume a cancelled or aborted run by using cached results in the working directory.
-c	string	Specifies a configuration file for preferred system specifications.
-work-dir	string	Default is the current directory. Specifying an alternate working directory can be useful on HPC systems to avoid storage limits on shared drives.