From fc84405d632efeac020b8d9331fb7141209c75f7 Mon Sep 17 00:00:00 2001
From: Peter Steinbach <steinbach@scionics.de>
Date: Thu, 4 Jun 2015 13:30:38 +0200
Subject: [PATCH] correct naming of output log depending on rule name
---
spim_registration/timelapse/Snakefile | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 8b4aa87..1cb115d 100644
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -11,17 +11,14 @@ configfile: "tomancak_czi.json"
padding_format = "{0:0"+str(padding_of_file_id(int(config["common"]["ntimepoints"])))+"d}"
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:
- #input: [ ds+"_fusion" for ds in datasets ]
- #input: [ ds + "_" + config["common"]["fusion_switch"] for ds in datasets ]
- #input: config["hdf5_output"]["output_xml"] + ".xml"
input: [ ds + "_output_hdf5" for ds in datasets ]
- #input: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
rule resave_prepared:
input: expand("{dataset}.{suffix}",dataset=[ config["common"]["hdf5_xml_filename"] ], suffix=["xml","h5"])
@@ -377,7 +374,7 @@ rule deconvolution:
rule define_output:
input: [ item + "_" + config["common"]["fusion_switch"] for item in datasets ], glob.glob('TP*')
output: config["hdf5_output"]["output_xml"].strip('\"') + ".xml"
- log: "define_xml_tif.log"
+ log: "define_output.log"
run:
cmd_string = produce_string(
"""{fiji-prefix} {fiji-app} \
--
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