diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile index e018c86443ab0ad1dc6e23abcc4f38d47402abd6..034c58b7c6b315ae3a3f4e9da1d6856f30a52f9f 100755 --- a/spim_registration/timelapse/Snakefile +++ b/spim_registration/timelapse/Snakefile @@ -1,5 +1,5 @@ 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}"