Uses now generic .yaml name

spim_registration/timelapse/Snakefile

@@ -13,7 +13,7 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
 # configfile: "dual_OneChannel.yaml"
 
 # data specific config file, expected to be inside JOBDIR
-configfile: "single.yaml"
+configfile: "config.yaml"
 
 padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
 ds_format = "-"+padding_format+"-00.h5"
@@ -26,9 +26,9 @@ xml_merge_in = produce_xml_merge_job_files(datasets)
 rule done:
     input: [ ds + "_output_hdf5" for ds in datasets ]
 
-<<<<<<< HEAD
-localrules: define_xml_tif, xml_merge, timelapse, 
-	    duplicate_transformations, external_transform, define_output
+# local rules are running the specified rules on the head node
+#localrules: define_xml_tif, xml_merge, timelapse, 
+#	    duplicate_transformations, external_transform, define_output
 	    
 rule resave_prepared:
     input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])

spim_registration/tools/master_preprocessing.sh

@@ -19,7 +19,7 @@
 #	channels are 0,1 etc
 # 
 #===============================================================================
-image_file_directory="/projects/pilot_spim/Christopher/cluster_test_HisYFP/2013-11-14_His-YFP_2/"
+image_file_directory="/projects/pilot_spim/Christopher/test_pipeline/dual_channel/tif_onefile/"
 
 # --- jobs directory -----------------------------------------------------------
 job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/tools/"
@@ -29,10 +29,10 @@ job_directory="/projects/pilot_spim/Christopher/snakemake-workflows/spim_registr
 # Important: For renaming and resaving .czi files the first .czi file has to
 # carry the index (0)
 #-------------------------------------------------------------------------------
-first_czi_name="2013-11-14_His-YFP_2.czi"
-timepoints="`seq 1 2`" # number of time points format: "`seq 0 1`"
+first_czi_name="2015-02-20_LZ2_Stock48_Stock58.czi"
+timepoints="`seq 0 1`" # number of time points format: "`seq 0 1`"
 angles="1 2 3 4 5" # angles format: "1 2 3"
-pad="2"		# for padded zeros
+pad="1"		# for padded zeros
 first_timepoint="0"	# Starts with 0
 #-------------------------------------------------------------------------------
 # Fiji settings