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Commit 7bc00304 authored by Peter Steinbach's avatar Peter Steinbach
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reducing .czi based rule on to first/head czi file given by config file

parent f5bf621e
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import os, glob, sys, re
from timelapse_utils import produce_xml_merge_job_files, produce_string, padding_of_file_id, glob_and_escape
from timelapse_utils import produce_xml_merge_job_files, produce_string, padding_of_file_id
#where are we (can be configured through -d/--directory flag)
JOBDIR=os.path.abspath(os.path.curdir)
......@@ -37,7 +37,7 @@ rule resave_prepared:
# defining xml for czi dataset
rule define_xml_czi:
input: glob_and_escape("*.czi"), config["common"]["first_czi"]
input: config["common"]["first_czi"]
output: config["common"]["first_xml_filename"] + ".xml"
log: "logs/a1_define_xml_czi.log"
run:
......@@ -510,7 +510,7 @@ rule resave_hdf5_output:
rule distclean:
params : glob.glob(config["common"]["hdf5_xml_filename"].strip('\"')+"*"), glob.glob(config["common"]["first_xml_filename"].strip('\"')+"*"), glob.glob("*registered"), glob.glob("*_fusion"), glob.glob("*_timelapse"), glob.glob("*log"), glob.glob("*_deconvolved"), glob.glob("*.xml~*"),"interestpoints", glob.glob("*empty"), expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]), glob.glob("*_output_hdf5"), glob.glob("*_output")# xml_merge_in,
params : glob.glob(config["common"]["hdf5_xml_filename"].strip('\"')+"*"), glob.glob(config["common"]["first_xml_filename"].strip('\"')+"*"), glob.glob("*registered"), glob.glob("*_fusion"), glob.glob("*_timelapse"), glob.glob("*log"), glob.glob("*_hdf5"), glob.glob("*_deconvolved"), glob.glob("*.xml~*"),"interestpoints", glob.glob("*empty"), expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]), glob.glob("*_output_hdf5"), glob.glob("*_output"), glob.glob("*.h5"), glob.glob("*.xml")
message : os.path.abspath(os.path.curdir) + ": rm -rf {params}"
shell : "rm -rf {params}"
......
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