Check consistency of flowdef and flowmat, using various rules.
check(x, ...)# S3 method for flowmat
check(x, ...)
# S3 method for flowdef
check(x, verbose = opts_flow$get("verbose"), ...)
a flowdef or flowmat object
Passed onto either check.flowdef OR check.flowmat functions
A numeric value indicating the amount of messages to produce.
Values are integers varying from 0, 1, 2, 3, .... Please refer to the verbose page for more details.
opts_flow$get("verbose")
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