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Published December 6, 2015 | Version 0.9.9.5
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flowr: flowr 0.9.9.5 (cherries)

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Description

flowr 0.9.9.5 (cherries)

2015-12-06

tl;dr (summary of changes)

  • Better handling of multiple flows in terms of running and re-running.
  • Nicer and cleaner messages.

additions/changes to flowr.conf file

  • New: option local_cores, which determines (max) number of cores to use when running local jobs.
  • New:: Now you can add a module_cmds variable to the config file, and this will be prefixed in all script of the pipeline. An example could be:

  • New: flow_pipe_paths now supports multiple paths, seperated by comma. The fetch_pipes() would split the vector at commas.

  • IMP: New version needs additional components in the flowr.conf file

# version >= 0.9.8.9004 # max number of cores to use when running on a local server local_cores 4 # default module of a pipeline # version >= 0.9.8.9015 module_cmds '' # examples: one may define all modules used in a pipeline here, # further one may specify any other command which should be run before # script executes. #module_cmds 'module load samtools;export PATH=$PATH:/apps/bin'

addition/changes to status()

  • New: status gets a new argument to turn off progress bar if needed.
  • New enhanced get_wds/status, so that if current wd contains a flow_details file, status is shown for this folder and not sub-folder(s).
## now this works well ! flowr status x=.

addition/changes to run() and rerun() functions

  • New: run function now accepts a custom configuration [conf], parameter. See help(flowr::run) for detail. The conf file would specify various parameters used for that pipeline.
  • New: run() re-running as well. i.e. One would generate a new set of commands etc. but execute in the previous folder; possibly from a inter-mediate step (trial feature).
  • New: Now rerun() supports multiple folders. Basically, one may specify a parent folder which has multiple flowr runs and ask it to re-run ALL of them again, from a specific intermediate step.
  • New: Flowr creates a new folder if there are multiple samples in the flowmat; basically containerizes the run, keeping the logs clean and debugging life easier.

other changes

  • New: to_flowdef() can now guess submission and dependency types (experimental feature).
  • IMP: to_flowdef now adds a parameter nodes, to enable specifying number of nodes required per-job.
  • IMP: opts_flow$get replaces get_opts, for reliability etc. Also this closely follows how knitr options are set.
  • fixed bugs in documentation (changed the formatting of output messages).

Files

flowr-0.9.9.5.zip

Files (1.8 MB)

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md5:6b729895c6e15862a51f72c292376174
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Additional details

Related works

Is supplement to
https://github.com/sahilseth/flowr/tree/0.9.9.5 (URL)