fixed wrong distclean target; fixed file_id increase through wildcards object; cleaned messages;

spim_registration/timelapse/Snakefile

@@ -43,7 +43,6 @@ rule resave_prepared:
 rule define_xml_czi:
     input: config["define_xml_czi"]["first_czi"]
     output: config["common"]["first_xml_filename"] + ".xml"
-    message: "Execute define_xml_czi on the following files {input}"
     log: "define_xml_czi.log"
     run: 
         cmd_string = produce_string(
@@ -70,14 +69,13 @@ rule define_xml_czi:
 	jdir=JOBDIR,
 	path_bsh=config["common"]["bsh_directory"] + config["define_xml_czi"]["bsh_file"])
 	
-	cmd_string += "> {log} 2>&1 && touch {output}"
+	cmd_string += " > {log} 2>&1"
         shell(cmd_string)
         
 # defining xml for tif dataset
 rule define_xml_tif:
     input: glob.glob('*.tif')
     output: config["common"]["first_xml_filename"] + ".xml"
-    message: "Execute define_xml_tif on the following files {input}"
     log: "define_xml_tif.log"
     run:
         cmd_string = produce_string(
@@ -104,7 +102,7 @@ rule define_xml_tif:
 	jdir=JOBDIR,
 	path_bsh=config["common"]["bsh_directory"] + config["define_xml_tif"]["bsh_file"])
 	
-	cmd_string +="> {log} 2>&1 && touch {output}"
+	cmd_string +=" > {log} 2>&1"
 	shell(cmd_string)
 
 ruleorder: define_xml_tif > define_xml_czi 
@@ -137,19 +135,18 @@ rule hdf5_xml:
            jdir=JOBDIR,
            path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"])
 
-        part_string += "> {log} 2>&1"
+        part_string += " > {log} 2>&1 && touch {output}"
         shell(part_string)
 
         #create dummy files according to the number of timepoints found
-        for index in range(int(config["common"]["ntimepoints"])):
-           shell("touch {basename}-0{file_id}-00.h5_empty".format(basename=config["common"]["hdf5_xml_filename"], file_id=index)) # problematic needs padding of file_id
+        # for index in range(int(config["common"]["ntimepoints"])):
+        #    shell("touch {basename}-0{file_id}-00.h5_empty".format(basename=config["common"]["hdf5_xml_filename"], file_id=index)) # problematic needs padding of file_id
         
 
 # resave .czi dataset as hdf5	
 rule resave_hdf5:
     input: "{xml_base}-{file_id,\d+}-00.h5_empty" # rules.hdf5_xml.output
     output: "{xml_base}-{file_id,\d+}-00.h5"
-    message: "Execute resave_hdf5 on {input}"
     log: "resave_hdf5-{file_id}.log"
     run:
         part_string = produce_string(
@@ -173,8 +170,8 @@ rule resave_hdf5:
            jdir=JOBDIR,
            path_bsh=config["common"]["bsh_directory"] + config["resave_hdf5"]["bsh_file"],
            input_xml_base="{wildcards.xml_base}",
-           job_number=int("{wildcards.file_id}")+1) # problematic calculation not possible in cannot deal wiht wildcards file_id
-   	part_string += "> {log} 2>&1"
+           job_number=int(wildcards.file_id)+1) # problematic calculation not possible in cannot deal wiht wildcards file_id
+   	part_string += " > {log} 2>&1"
         shell(part_string) 
        	       	
 rule registration:
@@ -395,4 +392,7 @@ rule deconvolution:
         shell(cmd_string)
   
 rule distclean:
-    shell : "rm -rf *registered *tif *log *_deconvolved *.xml~* interestpoints "+str(" ".join(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("*log"), glob.glob("*_deconvolved"), glob.glob("*.xml~*"),"interestpoints", glob.glob("*empty"), expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"])# xml_merge_in, 
+   
+    message : "removing {params}"
+    shell : "rm -rf {params}"