Workflows (and common use cases)

What is a workflow?

Good question! A workflow is a text-file that specified command-line options and input sequences required to run metAMOS. A workflow may optionally inherit options/data from other workflows. A workflow may also be immutable if the parameters should not be modifiable by a user.

Example workflow

An example workflow:

inherit:            isolate
modify:             True
command:            -q -u -r -v -I -c kraken -p 16 -a spades,velvet-sc,abyss,ray,edena,sga,masurca,soap,soap2,velvet -t metamos -n FunctionalAnnotation -f Postprocess -z phylum
asmcontigs:         /Users/skoren/Personal/Research/metAMOS/Test/test.asm,
lib1format:         fasta
lib1mated:          True
lib1innie:          True
lib1interleaved:    True
lib1f1:             /Users/skoren/Personal/Research/metAMOS/Test/carsonella_pe_filt.fna.gz,2000,5000,3500,500

Available options

The available options are:

  • inherit - any other workflows to inherit from. In this case, the workflow inherits options from the isolate workflow
  • modify - whether users are allowed to specify command-line parameters at runtime. If false, command-line options are ignored
  • command - command-line options to specify for runPipeline
  • asmcontigs - optional, pre-assembled contigs to include in analysis. Can be remote file. Multiple files can be separated using commas.
  • lib#format - input type for lib #. Can be fasta/fastq/sff
  • lib#mated - whether the library is mated or not
  • lib#innie - whether the mates are in the innie (Illumina paired-end) format or not (Illumina mate-pair)
  • lib#interleaved - whether the input sequences are in a single file or in two separate files
  • lib#f1 - the name of the input file, along with library min, max, mean, stdev

An arbitrary number of libraries may be specified in the above format. The below example shows an unmated library:

lib1format:         fasta
lib1mated:          False
lib1innie:          False
lib1interleaved:    False
lib1frg:            /Users/skoren/Personal/Research/metAMOS/Test/carsonella_pe_filt.fna.gz

as well as a non-interleaved library:

lib1format:         fasta
lib1mated:          True
lib1innie:          True
lib1interleaved:    False
lib1f1:             /Users/skoren/Personal/Research/metAMOS/Test/carsonella_pe_1.fna.gz,2000,5000,3500,500
lib1f2:             /Users/skoren/Personal/Research/metAMOS/Test/carsonella_pe.2.fna.gz,2000,5000,3500,500

Sharing your favorite MA workflows with others

Workflows may be shared between users, as long as the input files are accessible (i.e. they are on a remote server or the systems share a file system). Workflow files should be placed in the metAMOS/workflows directory or the working directory where MetAMOS is launched.