From 812abdc7acc69093216b42cdef9dca8d03b0be37 Mon Sep 17 00:00:00 2001
From: Christopher Schmied <schmied@mpi-cbg.de>
Date: Thu, 9 Jul 2015 21:32:36 +0200
Subject: [PATCH] Fixed bug in Snake file for TEMP files
Now recongnizes only first .czi file and fixes first job bug
---
spim_registration/timelapse/Snakefile | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/spim_registration/timelapse/Snakefile b/spim_registration/timelapse/Snakefile
index 588330f..39cf6ae 100755
--- a/spim_registration/timelapse/Snakefile
+++ b/spim_registration/timelapse/Snakefile
@@ -37,7 +37,7 @@ rule resave_prepared:
# defining xml for czi dataset
rule define_xml_czi:
- input: glob_and_escape("*.czi"), config["common"]["first_czi"]
+ input: config["common"]["first_czi"]
output: temp(config["common"]["first_xml_filename"] + ".xml")
log: "logs/a1_define_xml_czi.log"
run:
@@ -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: "{xml_base}.job_{file_id,\d+}.xml" #, "{xml_base}-{file_id,\d+}-00.h5_registered",
+ output: temp("{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(
@@ -477,7 +477,7 @@ rule hdf5_xml_output:
shell(part_string)
rule resave_hdf5_output:
- input: rules.hdf5_xml_output.output
+ input: rules.hdf5_xml_output.output, config["common"]["output_xml"].strip('\"') + ".xml"
output: temp("{xml_base}-{file_id,\d+}-00.h5_output_hdf5")
log: "logs/f3_resave_output-{file_id}.log"
run:
--
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