Log files are written into log directory in data directory

Log files are ordered

spim_registration/timelapse/Snakefile

@@ -34,7 +34,7 @@ rule resave_prepared:
 rule define_xml_czi:
     input:glob.glob('*.czi'), config["common"]["first_czi"]
     output: config["common"]["first_xml_filename"] + ".xml"
-    log: "define_xml_czi.log"
+    log: "logs/a1_define_xml_czi.log"
     run: 
         cmd_string = produce_string("""{fiji-prefix} {fiji-app} \
         -Dimage_file_directory={jdir} \
@@ -62,7 +62,7 @@ rule define_xml_czi:
 rule define_xml_tif:
     input: glob.glob(re.sub("{{.}}","*",config["common"]['image_file_pattern'])) #replaces all occurrences of {{a}} (a can be any character) by * to use the string for globbing
     output: config["common"]["first_xml_filename"] + ".xml"
-    log: "define_xml_tif.log"
+    log: "logs/a2_define_xml_tif.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -101,7 +101,7 @@ rule hdf5_xml:
     input: config["common"]["first_xml_filename"] + ".xml" 
     output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
             [ item+"_xml" for item in datasets ]
-    log: "hdf5_xml.log"
+    log: "logs/b1_hdf5_xml.log"
     run:
         part_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -131,7 +131,7 @@ rule hdf5_xml:
 rule resave_hdf5:
     input: rules.hdf5_xml.output # "{xml_base}-{file_id,\d+}-00.h5_xml"
     output: "{xml_base}-{file_id,\d+}-00.h5", "{xml_base}-{file_id,\d+}-00.h5_hdf5"
-    log: "resave_hdf5-{file_id}.log"
+    log: "logs/b2_resave_hdf5-{file_id}.log"
     run:
         part_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -160,7 +160,7 @@ rule resave_hdf5:
 rule registration:
     input:  "{xml_base}-{file_id}-00.h5" 
     output: "{xml_base}.job_{file_id,\d+}.xml"#, "{xml_base}-{file_id,\d+}-00.h5_registered", 
-    log: "{xml_base}-{file_id}-registration.log"
+    log: "logs/c_{xml_base}-{file_id}-registration.log"
     run:
         cmd_string = produce_string(
            """{fiji-prefix} {fiji-app} \
@@ -214,7 +214,7 @@ rule registration:
 rule xml_merge:
     input: [ str(config["common"]["hdf5_xml_filename"].strip('\"')+".job_"+(padding_format.format(item))+".xml") for item in range(int(config["common"]["ntimepoints"])) ] #[ item+"_registered" for item in datasets ] 
     output: "{xml_base}_merge.xml"
-    log: "{xml_base}_merge.log"
+    log: "logs/d1_{xml_base}_merge.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -232,7 +232,7 @@ rule xml_merge:
 rule timelapse:
     input: rules.xml_merge.output
     output: rules.xml_merge.output[0] + "_timelapse"
-    log: "{xml_base}_timelapse.log"
+    log: "logs/d2_{xml_base}_timelapse.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -265,7 +265,7 @@ rule timelapse:
 rule duplicate_transformations:
     input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
     output: rules.timelapse.output[0] + "_duplicate"
-    log: "{xml_base}_duplicate_transformations.log"
+    log: "logs/d3_{xml_base}_duplicate_transformations.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -292,7 +292,7 @@ rule duplicate_transformations:
 rule fusion:
     input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
     output: "{xml_base}-{file_id,\d+}-00.h5_fusion"
-    log: "{xml_base}-{file_id,\d+}-00-fusion.log"
+    log: "logs/e1_{xml_base}-{file_id,\d+}-00-fusion.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -335,7 +335,7 @@ rule fusion:
 rule external_transform:
     input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
     output: rules.timelapse.output[0] + "_external_trafo"
-    log: "external_transform.log"
+    log: "logs/e2_external_transform.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -363,7 +363,7 @@ rule external_transform:
 rule deconvolution:
     input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] ) ], "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.timelapse.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml" # rules.external_transform.output, "{xml_base}-{file_id,\d+}-00.h5", merged_xml="{xml_base}_merge.xml"
     output: "{xml_base}-{file_id,\d+}-00.h5_deconvolution"
-    log: "{xml_base}-{file_id,\d+}-00-deconvolution.log"
+    log: "logs/e2_{xml_base}-{file_id,\d+}-00-deconvolution.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -410,7 +410,7 @@ rule deconvolution:
 rule define_output:
     input: [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], glob.glob('TP*')
     output: config["common"]["output_xml"].strip('\"') + ".xml"
-    log: "define_output.log"
+    log: "logs/f1_define_output.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -443,7 +443,7 @@ rule hdf5_xml_output:
     input: config["common"]["output_xml"].strip('\"') + ".xml"
     output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
     	    [ item+"_output" for item in datasets ] 
-    log: "output_hdf5_xml.log"
+    log: "logs/f2_output_hdf5_xml.log"
     run:
         part_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \
@@ -474,7 +474,7 @@ rule hdf5_xml_output:
 rule resave_hdf5_output:
     input: rules.hdf5_xml_output.output
     output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
-    log: "resave_output-{file_id}.log"
+    log: "logs/f3_resave_output-{file_id}.log"
     run:
         part_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \