Merge branch 'master' of https://github.com/mpicbg-scicomp/snakemake-workflows...

Merge branch 'master' of https://github.com/mpicbg-scicomp/snakemake-workflows into mpicbg-scicomp-master

Conflicts:
	spim_registration/timelapse/Snakefile
	spim_registration/timelapse/single_test.yaml

spim_registration/timelapse/Snakefile

 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)
@@ -26,6 +26,7 @@ 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
 	    
@@ -34,6 +35,7 @@ rule resave_prepared:
 
 # defining xml for czi dataset
 rule define_xml_czi:
+
     input: config["common"]["first_czi"]
     output: temp(config["common"]["first_xml_filename"] + ".xml")
     log: "logs/a1_define_xml_czi.log"
@@ -107,7 +109,7 @@ rule hdf5_xml:
     log: "logs/b1_hdf5_xml.log"
     run:
         part_string = produce_string(
-        	"""{fiji-prefix} {fiji-app} \
+        	"""{fiji-prefix} {sysconfcpus} {num_cores_hdf5_xml} {fiji-app} \
                 -Dimage_file_directory={jdir} \
                 -Dfirst_xml_filename={first_xml_filename} \
                 -Dhdf5_xml_filename={hdf5_xml_filename} \
@@ -137,7 +139,7 @@ rule resave_hdf5:
     log: "logs/b2_resave_hdf5-{file_id}.log"
     run:
         part_string = produce_string(
-        	"""{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+        	"""{fiji-prefix} {sysconfcpus} {num_cores_resave_hdf5} {fiji-app} \
         	-Dimage_file_directory={jdir} \
                 -Dfirst_xml_filename={first_xml_filename} \
                 -Dhdf5_xml_filename={input_xml_base} \
@@ -166,7 +168,7 @@ rule registration:
     log: "logs/c_{xml_base}-{file_id}-registration.log"
     run:
         cmd_string = produce_string(
-           """{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+           """{fiji-prefix} {sysconfcpus} {num_cores_reg} {fiji-app} \
         -Dparallel_timepoints={file_id_w} \
         -Dimage_file_directory={jdir} \
         -Dxml_filename={input_xml} \
@@ -298,7 +300,7 @@ rule fusion:
     log: "logs/e1_{xml_base}-{file_id,\d+}-00-fusion.log"
     run:
         cmd_string = produce_string(
-        	"""{fiji-prefix} sysconfcpus -n 6 {fiji-app} \
+        	"""{fiji-prefix} {sysconfcpus} {num_cores_fusion} {fiji-app} \
         -Dimage_file_directory={jdir} \
     	-Dparallel_timepoints={file_id_w} \
     	-Dmerged_xml={merged_xml_file} \
@@ -369,7 +371,7 @@ rule deconvolution:
     log: "logs/e2_{xml_base}-{file_id,\d+}-00-deconvolution.log"
     run:
         cmd_string = produce_string(
-        	"""{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+        	"""{fiji-prefix} {sysconfcpus} {num_cores_deco} {fiji-app} \
         -Dimage_file_directory={jdir} \
         -Ddeco_output_file_directory={jdir} \
         -Dmerged_xml={merged_xml_file} \
@@ -449,7 +451,7 @@ rule hdf5_xml_output:
     log: "logs/f2_output_hdf5_xml.log"
     run:
         part_string = produce_string(
-        	"""{fiji-prefix} {fiji-app} \
+        	"""{fiji-prefix} {sysconfcpus} {num_cores_hdf5_xml_output} {fiji-app} \
                 -Dimage_file_directory={jdir} \
                 -Dfirst_xml_filename={output_xml} \
                 -Dhdf5_xml_filename={output_hdf5_xml} \
@@ -480,7 +482,7 @@ rule resave_hdf5_output:
     log: "logs/f3_resave_output-{file_id}.log"
     run:
         part_string = produce_string(
-        	"""{fiji-prefix} sysconfcpus -n 2 {fiji-app} \
+        	"""{fiji-prefix} {sysconfcpus} {num_cores_resave_hdf5_output} {fiji-app} \
                 -Dimage_file_directory={jdir} \
                 -Dfirst_xml_filename={output_xml} \
                 -Dhdf5_xml_filename={output_hdf5_xml} \
@@ -508,7 +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}"