From be543388da50ba20e8affb9193a711c31b6564c4 Mon Sep 17 00:00:00 2001
From: Bugra Oezdemir <bugra.oezdemir@embl.de>
Date: Thu, 20 Apr 2023 17:58:36 +0200
Subject: [PATCH] lowercase

---
 bin/__pycache__/PatternHandler.cpython-39.pyc | Bin
 bin/batchconvert_cli.sh                       |   2 +-
 bin/nextflow_cli.sh                           |   2 +-
 params/params.json                            |  10 +++++-----
 pythonexe                                     |   1 -
 5 files changed, 7 insertions(+), 8 deletions(-)
 mode change 100644 => 100755 bin/__pycache__/PatternHandler.cpython-39.pyc
 delete mode 120000 pythonexe

diff --git a/bin/__pycache__/PatternHandler.cpython-39.pyc b/bin/__pycache__/PatternHandler.cpython-39.pyc
old mode 100644
new mode 100755
diff --git a/bin/batchconvert_cli.sh b/bin/batchconvert_cli.sh
index 130d8a0..ceddcbe 100755
--- a/bin/batchconvert_cli.sh
+++ b/bin/batchconvert_cli.sh
@@ -1,2 +1,2 @@
 #!/usr/bin/env bash
-bfconvert $1 $2
\ No newline at end of file
+bioformats2raw $1 $2
\ No newline at end of file
diff --git a/bin/nextflow_cli.sh b/bin/nextflow_cli.sh
index dda48f2..c85db59 100755
--- a/bin/nextflow_cli.sh
+++ b/bin/nextflow_cli.sh
@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 SCRIPTPATH=$( dirname -- ${BASH_SOURCE[0]}; );
-nextflow -C $SCRIPTPATH/../configs/bftools.config -log $SCRIPTPATH/../WorkDir/logs/.nextflow.log run $SCRIPTPATH/../pff2ometiff.nf -params-file $SCRIPTPATH/../params/params.json -profile singularity;
+nextflow -C $SCRIPTPATH/../configs/bftools.config -log $SCRIPTPATH/../WorkDir/logs/.nextflow.log run $SCRIPTPATH/../pff2omezarr.nf -params-file $SCRIPTPATH/../params/params.json -profile singularity;
 nextflow clean but none -n -f;
\ No newline at end of file
diff --git a/params/params.json b/params/params.json
index 3e4269c..5e5f3b5 100755
--- a/params/params.json
+++ b/params/params.json
@@ -1,7 +1,7 @@
 {
-  "in_path": "/home/oezdemir/PycharmProjects/nfprojects/test",
-  "out_path": "/home/oezdemir/PycharmProjects/nfprojects/res1",
-  "pattern": "",
+  "in_path": "/home/oezdemir/PycharmProjects/nfprojects/data",
+  "out_path": "/home/oezdemir/PycharmProjects/nfprojects/results/zarr/res1",
+  "pattern": ".oir",
   "profile": "singularity",
   "source_type": "local",
   "dest_type": "local",
@@ -9,8 +9,8 @@
   "submit_rate_limit": "10/2min",
   "cluster_options": "--mem-per-cpu=3140 --cpus-per-task=16",
   "time": "6h",
-  "output_type": "ometiff",
+  "output_type": "omezarr",
   "reject_pattern": "",
-  "merge_files": "True",
+  "merge_files": "False",
   "concatenation_order": "auto"
 }
\ No newline at end of file
diff --git a/pythonexe b/pythonexe
deleted file mode 120000
index 453df9b..0000000
--- a/pythonexe
+++ /dev/null
@@ -1 +0,0 @@
-/home/oezdemir/anaconda3/envs/nfprojects/bin/python
\ No newline at end of file
-- 
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