flowr

Streamlining Workflows

Sahil Seth

r Sys.Date()

flowr 0.9.11

2021-03-01

added ability to toml files
bugfix in for moab and sge schedulers (see #74 for details)
bugfix in SBATCH params
bugfix #91
add ability to parse LSF resource output
Several other bug fixes: from @sbamin fix #73, #74, #83

flowr 0.9.10.9022

2017-04-30

bugfix in for moab and sge schedulers (see #74 for details)

flowr 0.9.10 (dates)

2016-04-18

tl;dr (summary of changes)

Flowr Rscript gets further enhancements, taking advantage of improved funr
run function now accepts paths.

# 'cherries' version
cd <path to pipelines>
flowr x=mypipeline

# 'dates' version
flowr x=<path to pipelines>/mypipeline

Previously, flowr expected a specific structure, now using ~/.flowr.conf, one may specify their own structure - enabling flexibility.

# 'cherries' version: a fixed directory structure was recommended:
~/flowr
├── conf
│   ├── flowr.conf
├── pipelines
│   ├── sleep_pipe.R
├── runs

# 'dates' version: one may change the default paths to run, config files etc using 
~/.flowr.conf

# this file controls the location of these folders:
flow_base_path  ~/flowr # flowr home
flow_conf_path  {{flow_base_path}}/conf  # path to configuration files, not required if using ~/.flowr.conf
flow_run_path   ~/flowr/runs  # default home of all executed flows, you may change this
flow_pipe_paths ~/flowr/pipelines,<add new paths...> # multiple paths can be specified using ","

a few bug fixes in to_flow
several other minor changes to messages, errors and warnings.

flowr 0.9.9.5 (cherries)

2015-12-03

tl;dr (summary of changes)

Better handling of multiple flows in terms of running and re-running.
Nicer and cleaner messages.
Add two additional lines in flowr.conf (modules_cmds and local_cores), after upgrading the package. Everything else is compatible with previous versions.

additions/changes to flowr.conf file

New: option local_cores, which determines (max) number of cores to use when running local jobs.
New: flow_pipe_paths now supports multiple paths, separated by comma. The fetch_pipes() would split the vector at commas.
IMP: New version needs additional components in the flowr.conf file
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:

# 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 more details. This enables one, to specify custom parameters used for that pipeline.
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.
New: run() now supports, 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 (experimental feature).

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).

flowr 0.9.8 (blueberries)

2015-10-02

Modified the output of status function, to add a status column. Specifically, this uses information from other columns and summarizes whether a specific step is pending, processing, completed or errored.

================================================================================
|                | total| started| completed| exit_status|status     |
|:---------------|-----:|-------:|---------:|-----------:|:----------|
|001.alnCmd1     |   109|     109|       109|           0|completed  |
|007.markCmd     |     3|       3|         0|           0|processing |

[0.9.7.11]
- Switched default value of flow@status to “created”.
- When using status on several folders, it used to be a little cluttered. Have added spaces, so that this looks prettier now.
Introducing verbose levels:

One can set the level of verboseness using opts_flow$set(verbose=2). Where the level may be 0, 1, 2…. Level 1 is good for most purposes, where as, level 0 is almost silent, producing messages only when necessary. While level 2 is good when developing a new pipeline, additional details useful for debugging are provided by level 3.
Detailed checking of flowdef

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

rerun [0.9.7.9021]:
- Previously one could specify a starting point from where a re-run flow would initiate execution. Now one may also specify an arbitrary number of of steps to re-run using select and ignore; which may need to run again.
job killing and submission now sport a progress bar:
- |============================================================ | 70%
- This is especially useful flows with thousands of jobs
Fixed 2 important bugs in moab.sh, lsf.sh template file, where it was missing the -n argument.
Now the status function has a new argument use_cache. If enabled, it skips fetching statuses of previously completed jobs; this really speeding things up.
- Also we have added a progress bar to show the status of this summarization.
Several detailed changes to the documentation.

flowr 0.9.7 (apples)

2015-08-22 (0.9.7.10)

This release adds and changes functionality of several functions.
A new function run(), creates and submits a pipeline. Specifically it follows the following steps:
- One supplies the name of the pipeline, which is used to fetch the pipeline using: fetch_pipe()
- create flowmat by running a function called mypipeline(), mypipeline is the name of the pipeline.
- load configuration file, with paths to tools etc using load_conf()
- fetch the flow definition using fetch_pipe, and load it using as.flowdef()
- Further, create a flow object using to_flow()
- Finally, submit to the cluster, submit_flow()
kill(): now a S3 functions, and operates on both a flow object and flow_wd folder
check(): Now works on flowdef and flowmat
as.flowmat(), as.flowdef(): easy ways to fetch and check these tables
fetch() along with fetch_pipes() and fetch_conf() simplify finding files
Reduce function overload, moving several functions a separate params pkg
- moved read_sheet(), write_sheet()
- moved get_opts(), set_opts()
- moved .load_conf() load_conf()
- Here is a link to params package
- kable function is now a part of params, that removes the dependency to knitr package
plot_flow: supports flowdef

flowr 0.9.6.13

[0.9.6.13] 2015-07-23
- Using PBS/LSF script instead of one line commands
- Format now a script, parsed using whisker
- to_flowmat() and to_flowdef() introduced; creating of these tables simplified
- Refactored code for plot_flow, handles multiple dependencies beautifully
[0.9.6.10] 2015-07-08
- add to_flow()
- kill_flow()
- supports moab
- burst as dependency type
- node can be character
- final job names changed to: sprintf(“%s_%s-%s”, basename(fobj@flow_path), jobj@jobname, i)
- Using PBS/LSF script instead of one line commands
- Format now a script, parsed using whisker

flowr 0.9.6.7

2015-04-07

add read_sample_sheet
clean package dependencies
[0.9.6.6]
- switch cat to messages
- added to_flow
[0.9.6.5]
- Added more examples
- Update Vignette with more examples
- squash issues in DESCRIPTION
[0.9.6.1]
- Added some vignettes for a simple and complex example
- satiate CRAN checks

flowr 0.9.5.1

2015-03-16

Added several new functions kill_flow(), which kills the flow.
Added experimental rerun_flow which still needs some work
updated documentation to satiate R CMD check
now job() checks for a dependency_type is previous job is provided
Added some slides inst
Integrated documentation with Sphnix
submit_flow, now generates flow_details.txt, flow.pdf, flow_status.txt
status() updates: flow_details.txt and flow_status.txt
save flow.rda files with all details on the flow
update flow details with job exit status, to be used in rerun

TODO

add more examples
update and cleanup documentation
integrate with sqlite with status
add example pipelines
assign UUID to each job/flow. and use that to track them.
Work on test_queue()
Add recipes

flowr 0.85

2014-12-05

get_flow_details():
Attach a job_number
Attach a flow level unique ID
update flow details with exited jobs
Create trigger upon start
add started/pending column in details and summary
plot_flow(): make plot type 1 as default
get_flow_status(): -exit_status: reports number of exited jobs (not sum of exit codes)

Versioning:

Loosely, following fruits A-Z.