bpipe-config

bpip-config is a configuration and reporting software for bpipe .

Repo: https://github.com/tucano/bpipe_config

bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as ‘pipelines’, see also the bpipe documentation

USAGE

Usage:

bpipe-config [options] [command] [pipeline_name] [sample_dirs|project_dirs]

List pipelines

Print a list of available pipelines:

bpipe-config -p

List commands

Print a list of available commands:

bpipe-config -c

OPTIONS

Available options:
 -b,--batch           Automatically execute bpipe in background (bg-bpipe)
 -c,--commands        Print a list of available commands
 -f,--force           Force files overwrite when needed (default=FALSE).
 -h,--help            Usage Information
 -m,--email <arg>     User email address (Es: -m user@example.com)
 -P,--project <arg>   Override the project name. If not provided will be extracted from SampleSheet in current
                      directory. Format: <PI_name>_<ProjectID>_<ProjectName>
 -p,--pipelines       Print a list of available pipelines
 -s,--skip-sheet      Skip SampleSheet checks
 -v,--verbose         Verbose mode

COMMANDS

Available Commands:
config    [dir1] [dir2] ...                       Configure current directory or directories in list (add
                                                  bpipe.config file).
pipe      <pipeline name> [dir1] [dir2] ...       Generate pipeline file in current directory or directories
                                                  in list (pipeline.groovy)
project   <pipeline name> [dir1] [dir2] ...       Generate a project pipeline for each directory in list
                                                  (pipeline.groovy)
sheet     <INFO> [dir1] [dir2] ...                Generate a SampleSheet.csv file using the INFO string in
                                                  current directory or directories in list. SampleProject
                                                  format: <PI_name>_<ProjectID>_<ProjectName>
info      <pipeline name> ...                     Get info on pipeline stages.
clean     [dir1] [dir2] ...                       Clean .bpipe dir in current working directory or in
                                                  directory list.
jvm                                               Get info on the JVM configuration
smerge    <Project1> <Project2> ...               Merge sample sheets from different Projects (for meta analysis)
json      <dir1> <dir2> ...                       Build a input.json file for manual branches definition

Use: bpipe-config info <pipeline name> to generate and html page with info for the pipeline.

sheet command INFO argument format:
    FCID=D2A8DACXX,Lane=3,SampleID=B1,SampleRef=hg19,Index=TTAGGC,Description=description,Control=N,Recipe=MeDIP,Operator=FG,SampleProject=PI_1A_name