check {flowr}

Check consistency of flowdef and flowmat

Description

Check consistency of flowdef and flowmat, using various rules.

Usage

check(x, ...)

## S3 method for class 'flowmat'
check(x, ...)

## S3 method for class 'flowdef'
check(x, verbose = opts_flow$get("verbose"), ...)

Arguments

x

a flowdef or flowmat object

...

Passed onto either check.flowdef OR check.flowmat functions

verbose

A numeric value indicating the amount of messages to produce. Values are integers varying from 0, 1, 2, 3, .... Please refer to the verbose page for more details. opts_flow$get("verbose")

Details

A typical output from flowdef with verbose level: 2

checking if required columns are present...
checking if resources columns are present...
checking if dependency column has valid names...
checking if submission column has valid names...
checking for missing rows in def...
checking for extra rows in def...
checking submission and dependency types...
jobname	prev.sub_type --> dep_type --> sub_type: relationship
1: aln1_a	none --> none --> scatter 
2: aln2_a	scatter --> none --> scatter 
3: sampe_a	scatter --> serial --> scatter rel: complex one:one
4: fixrg_a	scatter --> serial --> scatter rel: complex one:one
5: merge_a	scatter --> gather --> serial rel: many:one
6: markdup_a	serial --> serial --> serial rel: simple one:one
7: target_a	serial --> serial --> serial rel: simple one:one
8: realign_a	serial --> burst --> scatter rel: one:many
9: baserecalib_a	scatter --> serial --> scatter rel: complex one:one
10: printreads_a	scatter --> serial --> scatter rel: complex one:one