From a810d4ca2121f10ec62159279e1ac66993573c4f Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Sun, 29 May 2022 13:05:34 +0200
Subject: [PATCH] align, combine, deskew, convert
---
Snakefile | 42 +++++++++++++++++++++++++++++++++++++++++-
1 file changed, 41 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 3c5cbcb..58ba2ed 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,8 +1,48 @@
+rule align_and_count:
+ input:
+ data="{folder}/BF_TRITC_maxZ.zarr",
+ concentrations="{folder}/../concentrations.yaml",
+ template="/pasteur/appa/homes/aaristov/Anchor/Lena/Data/template16_pad100-adj.tif",
+ labels="/pasteur/appa/homes/aaristov/Anchor/Lena/Data/labels_bin2+100.tif"
+ output:
+ directory("{folder}/BF_TRITC_aligned.zarr")
+ log:
+ "{folder}/snakemake_align_n_count.log"
+ shell:
+ "srun -c 12 python align.py {input.data} {output} {input.concentrations} {input.template} {input.labels} 0"
+
+
rule get_sizes_nd2:
input:
"{file}.nd2"
output:
"{file}-sizes.txt"
shell:
- "python -c 'import nd2; print(nd2.ND2File({input}).sizes)' > {output}"
+ "python sizes.py {input} > {output}"
+
+rule combine_BF_TRITC_3D_maxZ:
+ input:
+ bf="{folder}/BF-2D.zarr",
+ fluo="{folder}/TRITC-3D.zarr"
+ output:
+ directory("{folder}/BF_TRITC_maxZ.zarr")
+ shell:
+ "srun -c 12 --job-name=maxZ python combine.py {input.bf} {input.fluo} {output}"
+
+
+rule convert_nd2_zarr:
+ input:
+ "{file}D.nd2"
+ output:
+ directory("{file}D.zarr")
+ shell:
+ "srun -c 12 --job-name=nd2-zarr singularity exec -B /pasteur /pasteur/appa/homes/aaristov/Anchor/Containers/zarr-tools_latest.sif python -m zarr_tools {input}"
+
+rule deskew:
+ input:
+ "{zarr}-skewed.zarr"
+ output:
+ directory("{zarr}.zarr")
+ shell:
+ "srun -c 12 --job-name=deskew python deskew.py {input} {output}"
\ No newline at end of file
--
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