diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 75dac119b8f76b60b8dbc336bc89bb1c44bab203..c52f49266afaaece165c8453e8f7dc46356443c8 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -20,7 +20,7 @@ ds_format = "-"+padding_format+"-00.h5"
# problematic needs padding of file_id
datasets = [ str(config["common"]["hdf5_xml_filename"].strip('\"')+(ds_format.format(item))) for item in range(int(config["common"]["ntimepoints"])) ]
-
+
xml_merge_in = produce_xml_merge_job_files(datasets)
rule done:
@@ -36,7 +36,7 @@ rule resave_prepared:
# defining xml for czi dataset
rule define_xml_czi:
input: config["common"]["first_czi"]
- output: temp(config["common"]["hdf5_xml_filename"].strip('\"') + "_first.xml")
+ output: config["common"]["hdf5_xml_filename"].strip('\"') + "_first.xml"
log: "logs/a1_define_xml_czi.log"
run:
cmd_string = produce_string(
@@ -67,7 +67,7 @@ rule define_xml_czi:
# defining xml for tif dataset
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: temp(config["common"]["hdf5_xml_filename"].strip('\"') + "_first.xml")
+ output: config["common"]["hdf5_xml_filename"].strip('\"') + "_first.xml"
log: "logs/a2_define_xml_tif.log"
run:
cmd_string = produce_string(
@@ -107,7 +107,7 @@ ruleorder: define_xml_czi > define_xml_tif
# create mother .xml/.h5
rule hdf5_xml:
input: config["common"]["hdf5_xml_filename"].strip('\"') + "_first.xml"
- output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]), temp([ item+"_xml" for item in datasets ])
+ output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]), [ item+"_xml" for item in datasets ]
log: "logs/b1_hdf5_xml.log"
run:
part_string = produce_string(
@@ -140,7 +140,7 @@ rule hdf5_xml:
# resave .czi/.tif dataset as hdf5
rule resave_hdf5:
input: "{xml_base}-{file_id,\d+}-00.h5_xml", config["common"]["hdf5_xml_filename"].strip('\"') + "_first.xml"
- output: "{xml_base}-{file_id,\d+}-00.h5", temp("{xml_base}-{file_id,\d+}-00.h5_hdf5")
+ output: "{xml_base}-{file_id,\d+}-00.h5", "{xml_base}-{file_id,\d+}-00.h5_hdf5"
log: "logs/b2_resave_hdf5-{file_id}.log"
run:
part_string = produce_string(
@@ -171,9 +171,9 @@ rule resave_hdf5:
shell(part_string)
rule registration:
- input: rules.resave_hdf5.output, [ item+"_hdf5" for item in datasets ], expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"])
- output: temp("{xml_base}.job_{file_id,\d+}.xml")
- log: "logs/c_{xml_base}-{file_id}-registration.log"
+ input: rules.resave_hdf5.output, expand("{dataset}_hdf5",dataset=datasets) , expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"])
+ output: "{xml_base}.job_{file_id,\d+}.xml"
+ log: "logs/c_{xml_base}-{file_id,\d+}-registration.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {sysconfcpus} {num_cores_reg} \
@@ -245,7 +245,7 @@ rule xml_merge:
rule timelapse:
input: rules.xml_merge.output
- output: temp(rules.xml_merge.output[0] + "_timelapse")
+ output: rules.xml_merge.output[0] + "_timelapse"
log: "logs/d2_{xml_base}_timelapse.log"
run:
cmd_string = produce_string(
@@ -280,7 +280,7 @@ rule timelapse:
rule duplicate_transformations:
input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
- output: temp(rules.timelapse.output[0] + "_duplicate")
+ output: rules.timelapse.output[0] + "_duplicate"
log: "logs/d3_{xml_base}_duplicate_transformations.log"
run:
cmd_string = produce_string(
@@ -307,7 +307,7 @@ 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: temp("{xml_base}-{file_id,\d+}-00.h5_fusion")
+ output: "{xml_base}-{file_id,\d+}-00.h5_fusion"
log: "logs/e1_{xml_base}-{file_id,\d+}-00-fusion.log"
run:
cmd_string = produce_string(
@@ -347,7 +347,7 @@ rule fusion:
rule external_transform:
input: rules.timelapse.output[0], merged_xml="{xml_base}_merge.xml"
- output: temp(rules.timelapse.output[0] + "_external_trafo")
+ output: rules.timelapse.output[0] + "_external_trafo"
log: "logs/e2_external_transform.log"
run:
cmd_string = produce_string(
@@ -376,7 +376,7 @@ rule external_transform:
rule deconvolution:
input: [ str("{xml_base}_merge.xml_" + config["common"]["transformation_switch"] + config["common"]["external_trafo_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: temp("{xml_base}-{file_id,\d+}-00.h5_deconvolution")
+ output: "{xml_base}-{file_id,\d+}-00.h5_deconvolution"
log: "logs/e2_{xml_base}-{file_id,\d+}-00-deconvolution.log"
run:
cmd_string = produce_string(
@@ -425,7 +425,7 @@ rule deconvolution:
rule define_output:
input: glob.glob('TP*'), [ item + "_" + config["common"]["fusion_switch"] for item in datasets ]
- output: temp(config["common"]["hdf5_xml_filename"].strip('\"') + "_output_define.xml")
+ output: config["common"]["hdf5_xml_filename"].strip('\"') + "_output_define.xml"
log: "logs/f1_define_output.log"
run:
cmd_string = produce_string(
@@ -461,7 +461,7 @@ rule define_output:
rule hdf5_xml_output:
input: glob.glob('TP*'), [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], config["common"]["hdf5_xml_filename"].strip('\"') + "_output_define.xml"
output: expand("{dataset}.{suffix}",dataset=[ config["common"]["fusion_switch"].strip('\"') + "_" + config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]),
- temp([ item+"_output" for item in datasets ])
+ [ item+"_output" for item in datasets ]
log: "logs/f2_output_hdf5_xml.log"
run:
part_string = produce_string(
@@ -496,7 +496,7 @@ rule hdf5_xml_output:
rule resave_hdf5_output:
input: "{xml_base}-{file_id,\d+}-00.h5_output", config["common"]["hdf5_xml_filename"].strip('\"') + "_output_define.xml"
- output: temp("{xml_base}-{file_id,\d+}-00.h5_output_hdf5")
+ output: "{xml_base}-{file_id,\d+}-00.h5_output_hdf5"
log: "logs/f3_resave_output-{file_id}.log"
run:
part_string = produce_string(