def add_archive_command(cmdparser):
"""Create a parser for the 'archive' command
"""
p = cmdparser.add_command('archive',help="Copy analyses to 'archive' area",
usage="%prog archive [OPTIONS] [ANALYSIS_DIR]",
version="%prog "+__version__,
description="Copy sequencing analysis data directory "
"ANALYSIS_DIR to 'archive' destination.")
p.add_option('--archive_dir',action='store',
dest='archive_dir',default=None,
help="specify top-level archive directory to copy data under. "
"ARCHIVE_DIR can be a local directory, or a remote location in the "
"form '[[user@]host:]directory'. Overrides the default settings.")
p.add_option('--platform',action='store',
dest='platform',default=None,
help="specify the platform e.g. 'hiseq', 'miseq' etc (overrides "
"automatically determined platform, if any). Use 'other' for cases "
"where the platform is unknown.")
p.add_option('--year',action='store',
dest='year',default=None,
help="specify the year e.g. '2014' (default is the current year)")
default_group = __settings.archive.group
p.add_option('--group',action='store',dest='group',default=default_group,
help="specify the name of group for the archived files NB only works "
"when the archive is a local directory (default: %s)" % default_group)
default_chmod = __settings.archive.chmod
p.add_option('--chmod',action='store',dest='chmod',default=default_chmod,
help="specify chmod operations for the archived files (default: "
"%s)" % default_chmod)
p.add_option('--force',action='store_true',dest='force',default=False,
help="perform archiving operation even if key metadata items are "
"not set")
add_dry_run_option(p)
add_debug_option(p)
def test_add_debug_option_with_argparse(self):
"""add_debug_option enables '--debug' with ArgumentParser
"""
p = ArgumentParser()
add_debug_option(p)
args = p.parse_args(['--debug'])
self.assertTrue(args.debug)
def add_publish_qc_command(cmdparser):
"""Create a parser for the 'publish_qc' command
"""
p = cmdparser.add_command('publish_qc',help="Copy QC reports to publication area",
usage="%prog publish_qc [OPTIONS] [ANALYSIS_DIR]",
description="Copy QC reports from ANALYSIS_DIR to local "
"or remote directory (e.g. web server). By default existing "
"QC reports will be copied without further checking; if no "
"report is found then QC results will be verified and a "
"report generated first.")
p.add_option('--projects',action='store',
dest='project_pattern',default=None,
help="simple wildcard-based pattern specifying a subset of projects "
"and samples to publish the QC for. PROJECT_PATTERN can specify a "
"single project, or a set of projects.")
p.add_option('--qc_dir',action='store',
dest='qc_dir',default=None,
help="specify target directory to copy QC reports to. QC_DIR can "
"be a local directory, or a remote location in the form "
"'[[user@]host:]directory'. Overrides the default settings.")
p.add_option('--ignore-missing-qc',action='store_true',
dest='ignore_missing_qc',default=False,
help="skip projects where QC results are missing or can't be verified, "
"or where reports can't be generated.")
p.add_option('--regenerate-reports',action='store_true',
dest='regenerate_reports',default=False,
help="attempt to regenerate existing QC reports")
p.add_option('--force',action='store_true',
dest='force',default=False,
help="force generation of QC reports for all projects even "
"if verification has failed")
add_debug_option(p)
def add_import_project_command(cmdparser):
"""Create a parser for the 'import_project' command
"""
p = cmdparser.add_command('import_project',help="Import a project directory",
usage="%prog import_project [OPTIONS] [ANALYSIS_DIR] PROJECT_DIR",
description="Copy a project directory PROJECT_DIR into "
"ANALYSIS_DIR.")
add_debug_option(p)
def test_add_debug_option(self):
"""add_debug_option enables '--debug'
"""
# Skip the test if optparse not available
if not OPTPARSE_AVAILABLE:
raise unittest.SkipTest("'optparse' not available")
p = OptionParser()
add_debug_option(p)
options, args = p.parse_args(['--debug'])
self.assertTrue(options.debug)
def add_samplesheet_command(cmdparser):
"""Create a parser for the 'samplesheet' command
"""
p = cmdparser.add_command('samplesheet',help="Sample sheet manipulation",
usage="%prog samplesheet [OPTIONS] [ANALYSIS_DIR]",
description="Query and manipulate sample sheets")
p.add_option('-e','--edit',action='store_true',dest='edit',default=False,
help="bring up sample sheet file in an editor to make "
"changes manually")
add_debug_option(p)
def add_params_command(cmdparser):
"""Create a parser for the 'params' command
"""
p = cmdparser.add_command('params',help="Query and change project parameters",
usage="%prog params [OPTIONS] [ANALYSIS_DIR]",
description="Query and change processing parameters "
"and settings for ANALYSIS_DIR.")
p.add_option('--set',action='append',dest='key_value',default=None,
help="Set the value of a parameter. KEY_VALUE should be of the form "
"'<param>=<value>'. Multiple --set options can be specified.")
add_debug_option(p)
def add_readme_command(cmdparser):
"""Create a parser for the 'readme' command
"""
p = cmdparser.add_command('readme',help="Add or amend top-level README file",
usage="%prog readme [OPTIONS] [ANALYSIS_DIR]",
description="Add or amend a README file in the "
"analysis directory DIR.")
p.add_option('--init',action='store_true',dest='init',default=False,
help="create a new README file")
p.add_option('--edit',action='store_true',dest='edit',default=False,
help="bring up README file in an editor to make changes")
add_debug_option(p)
def add_clone_command(cmdparser):
"""Create a parser for the 'clone' command
"""
p = cmdparser.add_command('clone',help="Make a copy of an analysis directory",
usage="%prog clone [OPTIONS] DIR CLONE_DIR",
description="Make a copy of an existing auto_processed analysis "
"directory DIR, in a new directory CLONE_DIR. The clone will "
"not include any project directories, but will copy the "
"projects.info file.")
p.add_option('--copy-fastqs',action='store_true',dest='copy_fastqs',default=False,
help="Copy fastq.gz files from DIR into DIR2 (default is to make a "
"link to the bcl-to-fastq directory)")
add_debug_option(p)
def add_metadata_command(cmdparser):
"""Create a parser for the 'metadata' command
"""
p = cmdparser.add_command('metadata',help="Query and update analysis metadata",
usage="%prog metadata [OPTIONS] [ANALYSIS_DIR]",
description="Query and change metadata "
"associated with ANALYSIS_DIR.")
p.add_option('--set',action='append',dest='key_value',default=None,
help="Set the value of a metadata item. KEY_VALUE should be of the form "
"'<param>=<value>'. Multiple --set options can be specified.")
p.add_option('--update',action='store_true',dest='update',default=False,
help="Automatically update metadata items where possible "
"(e.g. for older analyses which have old or missing metadata "
"files)")
add_debug_option(p)
def add_merge_fastq_dirs_command(cmdparser):
"""Create a parser for the 'merge_fastq_dirs' command
"""
p = cmdparser.add_command('merge_fastq_dirs',help="Combine bcl-to-fastq runs",
usage="%prog merge_fastq_dirs [OPTIONS] [ANALYSIS_DIR]",
description="Automatically merge fastq directories from "
"multiple bcl-to-fastq runs within ANALYSIS_DIR. Use this "
"command if 'make_fastqs' step was run multiple times to "
"process subsets of lanes.")
p.add_option('--primary-unaligned-dir',action='store',
dest='unaligned_dir',default='bcl2fastq',
help="merge fastqs from additional bcl-to-fastq directories into "
"UNALIGNED_DIR. Original data will be moved out of the way first. "
"Defaults to 'bcl2fastq'.")
add_dry_run_option(p)
add_debug_option(p)
def add_report_command(cmdparser):
"""Create a parser for the 'report' command
"""
p = cmdparser.add_command('report',help="Generate reporting information",
usage="%prog report [OPTIONS] [ANALYSIS_DIR]",
description="Report information on processed Illumina "
"sequence data in ANALYSIS_DIR.")
p.add_option('--logging',action='store_true',dest='logging',default=False,
help="print short report suitable for logging file")
p.add_option('--summary',action='store_true',dest='summary',default=False,
help="print full report suitable for bioinformaticians")
p.add_option('--projects',action='store_true',dest='projects',default=False,
help="print tab-delimited line (one per project) suitable for "
"injection into a spreadsheet")
p.add_option('--full',action='store_true',dest='full',default=False,
help="print summary report suitable for record-keeping")
add_debug_option(p)
def add_analyse_barcodes_command(cmdparser):
"""Create a parser for the 'analyse_barcodes' command
"""
p = cmdparser.add_command('analyse_barcodes',help="Analyse index (barcode) sequences",
usage="%prog analyse_barcodes [OPTIONS] [ANALYSIS_DIR]",
version="%prog "+__version__,
description="Analyse barcode sequences for fastq files "
"in specified lanes in ANALYSIS_DIR, and report the most "
"common barcodes found across all reads from each lane.")
p.add_option('--unaligned-dir',action='store',
dest='unaligned_dir',default='bcl2fastq',
help="explicitly set the (sub)directory with bcl-to-fastq outputs")
p.add_option('--lanes',action='store',
dest='lanes',default=None,
help="specify which lanes to analyse barcodes for (default is to do "
"analysis for all lanes).")
p.add_option('--mismatches',action='store',dest='mismatches',
default=0,type='int',
help="maximum number of mismatches to use when grouping "
"similar barcodes (default is 0, i.e. no grouping)")
p.add_option('--cutoff',action='store',dest='cutoff',
default=0.001,type='float',
help="exclude barcodes with a smaller fraction of "
"associated reads than CUTOFF, e.g. '0.01' excludes "
"barcodes with < 1% of reads (default is 0.01%)")
p.add_option('--sample-sheet',action="store",
dest="sample_sheet",default=None,
help="use an alternative sample sheet to the default "
"'custom_SampleSheet.csv' created on setup.")
p.add_option('--barcode-analysis-dir',action="store",
dest="barcode_analysis_dir",default=None,
help="specify subdirectory where barcode analysis will "
"be performed and outputs will be written")
add_runner_option(p)
add_debug_option(p)
# Deprecated options
deprecated = optparse.OptionGroup(p,'Deprecated/defunct options')
deprecated.add_option('--nprocessors',action='store',
dest='nprocessors',default=None,type='int',
help="does nothing; kept for backwards "
"compatibility only")
deprecated.add_option('--truncate',action='store',
dest='length',default=None,type='int',
help="does nothing; kept for backwards "
"compatibility only")
p.add_option_group(deprecated)
def add_setup_command(cmdparser):
"""Create a parser for the 'setup' command
"""
p = cmdparser.add_command('setup',help="Set up a new analysis directory",
usage="%prog setup [OPTIONS] DIR",
description="Set up automatic processing of Illumina "
"sequencing data from DIR.")
p.add_option('--sample-sheet',action='store',dest='sample_sheet',default=None,
help="Copy sample sheet file from name and location SAMPLE_SHEET "
"(default is to look for SampleSheet.csv inside DIR)")
p.add_option('--fastq-dir',action='store',dest='fastq_dir',default=None,
help="Import fastq.gz files from FASTQ_DIR (which should be a "
"subdirectory of DIR with the same structure as that produced "
"by CASAVA/bcl2fastq i.e. 'Project_<name>/Sample_<name>/<fastq>')")
p.add_option('--analysis-dir',action='store',dest='analysis_dir',default=None,
help="Make new directory called ANALYSIS_DIR (otherwise default is "
"'DIR_analysis')")
add_debug_option(p)
def add_update_fastq_stats_command(cmdparser):
"""Create a parser for the 'update_fastq_stats' command
"""
p = cmdparser.add_command('update_fastq_stats',help="(Re)generate Fastq statistics",
usage="%prog update_fastq_stats [OPTIONS] [ANALYSIS_DIR]",
description="(Re)generate statistics for fastq "
"files produced from 'make_fastqs'.")
p.add_option('--unaligned-dir',action='store',
dest='unaligned_dir',default='bcl2fastq',
help="explicitly set the (sub)directory with bcl-to-fastq outputs")
p.add_option('--stats-file',action='store',
dest='stats_file',default=None,
help="specify output file for fastq statistics")
p.add_option('--per-lane-stats-file',action='store',
dest='per_lane_stats_file',default=None,
help="specify output file for per-lane statistics")
add_nprocessors_option(p,__settings.fastq_stats.nprocessors)
add_runner_option(p)
add_debug_option(p)
def add_setup_analysis_dirs_command(cmdparser):
"""Create a parser for the 'setup_analysis_dirs' command
"""
p = cmdparser.add_command('setup_analysis_dirs',help="Create project subdirectories",
usage="%prog setup_analysis_dirs [OPTIONS] [ANALYSIS_DIR]",
description="Create analysis subdirectories for projects "
"defined in projects.info file in ANALYSIS_DIR.")
p.add_option('--ignore-missing-metadata',action='store_true',
dest='ignore_missing_metadata',default=False,
help="force creation of project directories even if metadata is not "
"set (default is to fail if metadata is missing)")
p.add_option('--short-fastq-names',action='store_true',
dest='short_fastq_names',default=False,
help="shorten fastq file names when copying or linking from project "
"directory (default is to keep long names from bcl2fastq)")
p.add_option('--link-to-fastqs',action='store_true',
dest='link_to_fastqs',default=False,
help="create symbolic links to original fastqs from project directory "
"(default is to make hard links)")
add_debug_option(p)
def add_config_command(cmdparser):
"""Create a parser for the 'config' command
"""
p = cmdparser.add_command('config',help="Query and change global configuration",
usage="%prog config [OPTIONS] [ANALYSIS_DIR]",
description="Query and change global configuration.")
p.add_option('--init',action='store_true',dest='init',default=False,
help="Create a new configuration file from the sample.")
p.add_option('--set',action='append',dest='key_value',default=None,
help="Set the value of a parameter. KEY_VALUE should be of the form "
"'<param>=<value>'. Multiple --set options can be specified.")
p.add_option('--add',action='append',dest='new_section',default=None,
help="Add a new section called NEW_SECTION to the config. To add a "
"new platform, use 'platform:NAME'. Multiple --add options can be "
"specified.")
add_debug_option(p)
# Deprecated options
deprecated = optparse.OptionGroup(p,'Deprecated/defunct options')
deprecated.add_option('--show',action='store_true',dest='show',default=False,
help="Show the values of parameters and settings (does "
"nothing; use 'config' with no options to display settings)")
p.add_option_group(deprecated)
def add_run_qc_command(cmdparser):
"""Create a parser for the 'run_qc' command
"""
p = cmdparser.add_command('run_qc',help="Run QC procedures",
usage="%prog run_qc [OPTIONS] [ANALYSIS_DIR]",
description="Run QC procedures for sequencing projects in "
"ANALYSIS_DIR.")
max_concurrent_jobs = __settings.general.max_concurrent_jobs
fastq_screen_subset = 1000000
p.add_option('--projects',action='store',
dest='project_pattern',default=None,
help="simple wildcard-based pattern specifying a subset of projects "
"and samples to run the QC on. PROJECT_PATTERN should be of the form "
"'pname[/sname]', where 'pname' specifies a project (or set of "
"projects) and 'sname' optionally specifies a sample (or set of "
"samples).")
p.add_option('--fastq_screen_subset',action='store',dest='subset',
type='int',default=fastq_screen_subset,
help="specify size of subset of total reads to use for "
"fastq_screen (i.e. --subset option); (default %d, set to "
"0 to use all reads)" % fastq_screen_subset)
p.add_option('--ungzip-fastqs',action='store_true',dest='ungzip_fastqs',
help="create decompressed copies of fastq.gz files")
p.add_option('--max-jobs',action='store',
dest='max_jobs',default=max_concurrent_jobs,type='int',
help="explicitly specify maximum number of concurrent QC jobs to run "
"(default %s, change in settings file)" % max_concurrent_jobs)
add_runner_option(p)
add_modulefiles_option(p)
add_debug_option(p)
# Deprecated options
deprecated = optparse.OptionGroup(p,'Deprecated/defunct options')
deprecated.add_option('--no-ungzip-fastqs',action='store_true',dest='no_ungzip_fastqs',
help="don't create uncompressed copies of fastq.gz files "
"(does nothing; this is now the default, use --ungzip-fastqs "
"to turn on decompression)")
p.add_option_group(deprecated)
def add_make_fastqs_command(cmdparser):
"""Create a parser for the 'make_fastqs' command
"""
p = cmdparser.add_command('make_fastqs',help="Run Fastq generation",
usage="%prog make_fastqs [OPTIONS] [ANALYSIS_DIR]",
description="Generate fastq files from raw bcl files "
"produced by Illumina sequencer within ANALYSIS_DIR.")
# General options
add_no_save_option(p)
add_modulefiles_option(p)
add_debug_option(p)
# Primary data management
primary_data = optparse.OptionGroup(p,'Primary data management')
primary_data.add_option('--only-fetch-primary-data',action='store_true',
dest='only_fetch_primary_data',default=False,
help="only fetch the primary data, don't perform any other "
"operations")
primary_data.add_option('--skip-rsync',action='store_true',
dest='skip_rsync',default=False,
help="don't rsync the primary data at the beginning of processing")
primary_data.add_option('--remove-primary-data',action='store_true',
dest='remove_primary_data',default=False,
help="Delete the primary data at the end of processing (default "
"is to keep data)")
p.add_option_group(primary_data)
# Options to control bcl2fastq
bcl_to_fastq = optparse.OptionGroup(p,'Bcl-to-fastq options')
bcl_to_fastq.add_option('--skip-bcl2fastq',action='store_true',
dest='skip_bcl2fastq',default=False,
help="don't run the Fastq generation step")
bcl_to_fastq.add_option('--output-dir',action='store',
dest='unaligned_dir',default=None,
help="explicitly set the output (sub)directory for bcl-to-fastq "
"conversion (overrides default)")
bcl_to_fastq.add_option('--use-bases-mask',action="store",
dest="bases_mask",default=None,
help="explicitly set the bases-mask string to indicate how each "
"cycle should be used in the bcl-to-fastq conversion (overrides "
"default)")
bcl_to_fastq.add_option('--sample-sheet',action="store",
dest="sample_sheet",default=None,
help="use an alternative sample sheet to the default "
"'custom_SampleSheet.csv' created on setup.")
bcl_to_fastq.add_option('--ignore-missing-bcl',action='store_true',
dest='ignore_missing_bcl',default=False,
help="use the --ignore-missing-bcl option for bcl2fastq (treat "
"missing bcl files as no call)")
bcl_to_fastq.add_option('--ignore-missing-stats',action='store_true',
dest='ignore_missing_stats',default=False,
help="use the --ignore-missing-stats option for bcl2fastq (fill "
"in with zeroes when *.stats files are missing)")
bcl_to_fastq.add_option('--require-bcl2fastq-version',action='store',
dest='bcl2fastq_version',default=None,
help="explicitly specify version of bcl2fastq "
"software to use (e.g. '1.8.4' or '>=2.0').")
# Use lane splitting
# Determine defaults to report to user
no_lane_splitting_platforms = []
use_lane_splitting_platforms = []
for platform in __settings.platform:
if __settings.platform[platform].no_lane_splitting is not None:
if __settings.platform[platform].no_lane_splitting:
no_lane_splitting_platforms.append(platform)
else:
use_lane_splitting_platforms.append(platform)
if __settings.bcl2fastq.no_lane_splitting:
if use_lane_splitting_platforms:
default_no_lane_splitting = \
"Used by default for all platforms except %s" % \
', '.join(use_lane_splitting_platforms)
default_use_lane_splitting = "Used by default for %s" % \
', '.join(use_lane_splitting_platforms)
else:
default_no_lane_splitting = "Default for all platforms"
default_use_lane_splitting = ""
else:
if no_lane_splitting_platforms:
default_use_lane_splitting = \
"Used by default for all platforms except %s" % \
', '.join(no_lane_splitting_platforms)
default_no_lane_splitting = "Used by default for %s" % \
', '.join(no_lane_splitting_platforms)
else:
default_no_lane_splitting = ""
default_use_lane_splitting = "Default for all platforms"
if default_use_lane_splitting:
default_use_lane_splitting = ". "+default_use_lane_splitting
if default_no_lane_splitting:
default_no_lane_splitting = ". "+default_no_lane_splitting
bcl_to_fastq.add_option('--no-lane-splitting',action='store_true',
dest='no_lane_splitting',default=False,
help="don't split the output FASTQ files by lane "
"(bcl2fastq v2 only; turn off using "
"--use-lane-splitting)%s" % default_no_lane_splitting)
bcl_to_fastq.add_option('--use-lane-splitting',action='store_true',
dest='use_lane_splitting',default=False,
help="split the output FASTQ files by lane "
"(bcl2fastq v2 only; turn off using "
"--no-lane-splitting)%s" % default_use_lane_splitting)
# Adapter trimming/masking options
bcl_to_fastq.add_option('--minimum-trimmed-read-length',action="store",
dest="minimum_trimmed_read_length",default=35,
help="Minimum read length after adapter "
"trimming. bcl2fastq trims the adapter from "
"the read down to this value; if there is more "
"adapter match below this length then those "
"bases are masked not trimmed (i.e. replaced "
"by N rather than removed) (default: 35)")
bcl_to_fastq.add_option('--mask-short-adapter-reads',action="store",
dest="mask_short_adapter_reads",default=22,
help="minimum length of unmasked bases that "
"a read can be after adapter trimming; reads "
"with fewer ACGT bases will be completely "
"masked with Ns (default: 22)")
# Creation of empty fastqs
bcl_to_fastq.add_option('--create-empty-fastqs',action='store_true',
dest='create_empty_fastqs',default=False,
help="create 'empty' FASTQ files which weren't "
"generated by bcl2fastq because they didn't "
"have any reads assigned at the demultiplexing "
"stage (NB bcl2fastq must have finished without "
"an error for this option to be applied)")
# Number of processors
default_nprocessors = []
for platform in __settings.platform:
if __settings.platform[platform].nprocessors is not None:
default_nprocessors.append("%s: %s" %
(platform,
__settings.platform[platform].nprocessors))
if default_nprocessors:
default_nprocessors.append("other platforms: %s" %
__settings.bcl2fastq.nprocessors)
else:
default_nprocessors.append("%s" % __settings.bcl2fastq.nprocessors)
default_nprocessors = ', '.join(default_nprocessors)
add_nprocessors_option(bcl_to_fastq,None,
default_display=default_nprocessors)
add_runner_option(bcl_to_fastq)
p.add_option_group(bcl_to_fastq)
# Statistics
statistics = optparse.OptionGroup(p,'Statistics generation')
statistics.add_option('--stats-file',action='store',
dest='stats_file',default=None,
help="specify output file for fastq statistics")
statistics.add_option('--per-lane-stats-file',action='store',
dest='per_lane_stats_file',default=None,
help="specify output file for per-lane statistics")
statistics.add_option('--no-stats',action='store_true',
dest='no_stats',default=False,
help="don't generate statistics file; use 'update_fastq_stats' "
"command to (re)generate statistics")
p.add_option_group(statistics)
# Deprecated options
deprecated = optparse.OptionGroup(p,'Deprecated/defunct options')
deprecated.add_option('--keep-primary-data',action='store_true',
dest='keep_primary_data',default=False,
help="don't delete the primary data at the end of processing "
"(does nothing; primary data is kept by default unless "
"--remove-primary-data is specified)")
deprecated.add_option('--generate-stats',action='store_true',
dest='generate_stats',default=False,
help="(re)generate statistics for fastq files (does nothing; "
"statistics are generated by default unless suppressed by "
"--no-stats)")
deprecated.add_option('--report-barcodes',action='store_true',
dest='report_barcodes',default=False,
help="analyse and report barcode indices for all lanes after "
"generating fastq files (deprecated: use the "
"'analyse_barcodes' command instead)")
deprecated.add_option('--barcodes-file',action='store',
dest='barcodes_file',default=None,
help="specify output file for barcode analysis report "
"(deprecated: use the 'analyse_barcodes' command instead)")
p.add_option_group(deprecated)
#######################################################################
# Main program
#######################################################################
if __name__ == "__main__":
# Set up command line parser
p = CommandParser(description="Utility for managing processed and analysed Illumina "
"sequence data in ANALYSIS_DIR",
version="%prog "+get_version())
# Add info command
p.add_command('info',help="Get information about ANALYSIS_DIR",
usage="%prog info [OPTIONS] ANALYSIS_DIR",
description="Report information on processed Illumina "
"sequence data in ANALYSIS_DIR.")
add_debug_option(p.parser_for('info'))
# Add copy command
p.add_command('copy',help="Copy fastqs from ANALYSIS_DIR",
usage="%prog copy [OPTIONS] ANALYSIS_DIR DEST_DIR",
description="Copy fastqs from ANALYSIS_DIR to DEST_DIR.")
p.parser_for('copy').add_option('--projects',action='store',dest='projects',default=None,
help="Restrict copying to projects matching the "
"supplied pattern")
p.parser_for('copy').add_option('--fastq-dir',action='store',dest='fastq_dir',default=None,
help="Only copy fastqs from the specified FASTQ_DIR")
add_dry_run_option(p.parser_for('copy'))
add_debug_option(p.parser_for('copy'))
# Process the command line
cmd,options,args = p.parse_args()
if len(args) < 1:
p.error("Need to supply a directory to examine")
