import sys
from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.srf import make_commands, run_srf_commands, pathname_to_run_name
+from htsworkflow.pipelines.srf import make_srf_commands, make_qseq_commands, \
+ run_commands, pathname_to_run_name
from htsworkflow.pipelines.srf import ILLUMINA2SRF10, ILLUMINA2SRF11, SOLEXA2SRF
def make_parser():
parser.error(
"Number of lane arguments must match number of runfolders"
)
-
+
+ make_commands = make_qseq_commands
# build list of commands
cmds = {}
for runfolder_path, lanes in zip(args, lanes_list):
return 1
elif len(runs) == 1:
bustard_dir = runs[0].bustard.pathname
- cmds[bustard_dir] = make_commands(run_name, lanes, opts.site, opts.dest_dir, opts.runfolder_version)
+ cmds[bustard_dir] = make_commands(run_name,
+ bustard_dir,
+ lanes,
+ opts.site,
+ opts.dest_dir,
+ opts.runfolder_version)
else:
print "ERROR: Couldn't find a bustard directory in", runfolder_path
return 1
if not opts.dry_run:
for cwd, cmd_list in cmds.items():
- run_srf_commands(cwd, cmd_list, opts.jobs)
+ run_commands(cwd, cmd_list, opts.jobs)
else:
for cwd, cmd_list in cmds.items():
print cwd