filter a matrix based on a minimum value and numbers of samples that must pass.
Input
name:type
description
pattern
meta:map
Groovy Map containing information on matrix to be filtered, at a
minimum an id. e.g. [ id:‘test’ ]
abundance:file
Raw TSV or CSV format abundance matrix with features (e.g.
genes) by row and observations (e.g. samples) by column. All rownames
from the sample sheet should be present in the columns.
samplesheet_meta:map
Where samplesheet is provided, aroovy Map containing information on
sample sheet, at a minimum an id. e.g. [ id:‘test’ ]
samplesheet:file
Optional CSV or TSV format sample sheet with sample metadata. If
provided this is used to infer minimum passing samples from group sizes
present (see grouping_variable), but also to validate matrix columns.
If not provided, all numeric columns are selected.
Output
name:type
description
pattern
filtered
meta:map
Groovy Map containing information on experiment.
e.g. [ id:‘test’ ]
*.filtered.tsv:file
Filtered version of input matrix
*.filtered.tsv
tests
meta:map
Groovy Map containing information on experiment.
e.g. [ id:‘test’ ]
*.tests.tsv:file
Boolean matrix with pass/ fail status for each test on each feature
*.tests.tsv
session_info
meta:map
Groovy Map containing information on experiment.
e.g. [ id:‘test’ ]
*R_sessionInfo.log:file
Log file containing R session information
*.log
versions
versions.yml:file
File containing software versions
versions.yml
Tools
matrixfilter
filter a matrix based on a minimum value and numbers of samples
