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 -- GitLab