diff --git a/config/config.yml b/config/config.yml index f1b67eb..3ac7293 100644 --- a/config/config.yml +++ b/config/config.yml @@ -162,5 +162,5 @@ report: containers: - spimprep: 'docker://khanlab/spimprep-deps:imaris-deps' + spimprep: 'docker://khanlab/spimprep-deps:v0.1.1' diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 155031a..a46a976 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -174,7 +174,7 @@ def get_input_sample(wildcards): # sample was a tar file, so point to the extracted folder return rules.extract_sample.output.ome_dir.format(**wildcards) - elif sample_path.suffixes[-1] == '.ims': + elif sample_path.suffixes[-1] == ".ims": return get_sample_path_remote(wildcards) else: print(f"unsupported input: {sample_path}") diff --git a/workflow/rules/imaris.smk b/workflow/rules/imaris.smk index f7c3b2d..b6f2c07 100644 --- a/workflow/rules/imaris.smk +++ b/workflow/rules/imaris.smk @@ -35,21 +35,24 @@ rule imaris_to_metadata: script: "../scripts/imaris_to_metadata.py" + rule imaris_channel_to_zarr: input: ims=get_input_sample, params: channel=lambda wildcards: get_stains(wildcards).index(wildcards.stain), output: - zarr=temp(bids( - root=work, - subject="{subject}", - datatype="micr", - sample="{sample}", - acq="{acq}", - stain="{stain}", - suffix="imaris.zarr.zip", - )), + zarr=temp( + bids( + root=work, + subject="{subject}", + datatype="micr", + sample="{sample}", + acq="{acq}", + stain="{stain}", + suffix="imaris.zarr.zip", + ) + ), log: bids( root="logs", @@ -68,22 +71,27 @@ rule imaris_channel_to_zarr: resources: runtime=360, mem_mb=1000, - shadow: 'minimal' + shadow: + "minimal" script: "../scripts/imaris_channel_to_zarr.py" rule imaris_to_ome_zarr: input: - zarr=lambda wildcards: expand(bids( - root=work, - subject="{subject}", - datatype="micr", - sample="{sample}", - acq="{acq}", - stain="{stain}", - suffix="imaris.zarr.zip", - ),stain=get_stains(wildcards),allow_missing=True), + zarr=lambda wildcards: expand( + bids( + root=work, + subject="{subject}", + datatype="micr", + sample="{sample}", + acq="{acq}", + stain="{stain}", + suffix="imaris.zarr.zip", + ), + stain=get_stains(wildcards), + allow_missing=True, + ), metadata_json=rules.prestitched_to_metadata.output.metadata_json, params: max_downsampling_layers=config["ome_zarr"]["max_downsampling_layers"], @@ -112,8 +120,7 @@ rule imaris_to_ome_zarr: resources: runtime=360, mem_mb=config["total_mem_mb"], - shadow: 'minimal' + shadow: + "minimal" script: "../scripts/imaris_to_ome_zarr.py" - - diff --git a/workflow/rules/ome_zarr.smk b/workflow/rules/ome_zarr.smk index 2313ff9..0516fac 100644 --- a/workflow/rules/ome_zarr.smk +++ b/workflow/rules/ome_zarr.smk @@ -89,7 +89,6 @@ rule tif_stacks_to_ome_zarr: "../scripts/tif_stacks_to_ome_zarr.py" - rule ome_zarr_to_nii: input: **get_storage_creds(), @@ -138,4 +137,3 @@ rule ome_zarr_to_nii: config["containers"]["spimprep"] script: "../scripts/ome_zarr_to_nii.py" -