diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile index 4a41cdee566275be5ef5ad1e0433bbf7fe9e3a0f..a5ebd42518aa56accd699958797eacaa87d58e55 100755 --- a/spim_registration/timelapse/Snakefile +++ b/spim_registration/timelapse/Snakefile @@ -38,7 +38,7 @@ rule resave_prepared: # defining xml for czi dataset rule define_xml_czi: input: glob_and_escape("*.czi"), config["common"]["first_czi"] - output: temp (config["common"]["first_xml_filename"] + ".xml") + output: temp(config["common"]["first_xml_filename"] + ".xml") log: "logs/a1_define_xml_czi.log" run: cmd_string = produce_string("""{fiji-prefix} {fiji-app} \ @@ -105,7 +105,7 @@ ruleorder: define_xml_czi > define_xml_tif rule hdf5_xml: input: config["common"]["first_xml_filename"] + ".xml" output: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]), - temp([ item+"_xml" for item in datasets ]) + [ item+"_xml" for item in datasets ] log: "logs/b1_hdf5_xml.log" run: part_string = produce_string( @@ -135,7 +135,7 @@ rule hdf5_xml: # resave .czi/.tif dataset as hdf5 rule resave_hdf5: input: rules.hdf5_xml.output, config["common"]["first_xml_filename"] + ".xml" # "{xml_base}-{file_id,\d+}-00.h5_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( @@ -164,7 +164,7 @@ rule resave_hdf5: rule registration: input: "{xml_base}-{file_id}-00.h5", expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"].strip('\"')], suffix=["xml","h5"]) - output: temp("{xml_base}.job_{file_id,\d+}.xml") #, "{xml_base}-{file_id,\d+}-00.h5_registered", + output: "{xml_base}.job_{file_id,\d+}.xml" #, "{xml_base}-{file_id,\d+}-00.h5_registered", log: "logs/c_{xml_base}-{file_id}-registration.log" run: cmd_string = produce_string( @@ -236,7 +236,7 @@ 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( @@ -296,7 +296,7 @@ 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( @@ -367,7 +367,7 @@ 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: 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( @@ -447,7 +447,7 @@ rule define_output: rule hdf5_xml_output: input: config["common"]["output_xml"].strip('\"') + ".xml" output: expand("{dataset}.{suffix}",dataset=[ config["common"]["output_hdf5_xml"].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( @@ -478,7 +478,7 @@ rule hdf5_xml_output: rule resave_hdf5_output: input: rules.hdf5_xml_output.output, rules.define_output.output - 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( @@ -520,5 +520,5 @@ rule distclean: # onsuccess: # shell("mail -s \"[SUCCESS] our_cluster:{jdir} finished \" schmied@mpi-cbg.de < /dev/null".format(jdir=JOBDIR)) -onerror: - shell("mail -s \"[ERROR] out_cluster:{jdir}\" schmied@mpi-cbg.de < /dev/null".format(jdir=JOBDIR)) +#onerror: +# shell("mail -s \"[ERROR] out_cluster:{jdir}\" schmied@mpi-cbg.de < /dev/null".format(jdir=JOBDIR))