diff --git a/.github/snakebids_action_requirements.txt b/.github/snakebids_action_requirements.txt
deleted file mode 100644
index bcfaa15..0000000
--- a/.github/snakebids_action_requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-snakebids @ git+https://github.com/khanlab/snakebids#8acbd9f
-typing-extensions = ">=3.10.0"
-attrs = ">=21.2.0"
-boutiques = "^0.5.25"
-more-itertools = ">=8"
-pvandyken-deprecated = "0.0.4" 
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 34af862..a272261 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -6,52 +6,42 @@ on:
   pull_request:
     branches: [ main ]
 
-
 jobs:
-  Formatting:
+  tests:
     runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Formatting
-        uses: github/super-linter@v4
-        env:
-          VALIDATE_ALL_CODEBASE: false
-          DEFAULT_BRANCH: main
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+    strategy:
+      max-parallel: 5
 
-  Linting:
-    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - name: Lint workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v2
       with:
-        directory: .
-        stagein: "pip install --no-deps -r .github/snakemake_action_requirements.txt"
-        snakefile: workflow/Snakefile
-        args: "--lint"
+        python-version: 3.11
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda install -c conda-forge mamba
+        #    - name: Lint with flake8
+        #      run: |
+        #        mamba install flake8
+        #        # stop the build if there are Python syntax errors or undefined names
+        #        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        #        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        #        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Setup snakemake and workflow dependencies
+      run: |
+        mamba install -c conda-forge -c bioconda pytest snakemake singularity snakefmt
+        pip install . 
+    - name: Lint with snakemake and snakefmt
+      run: |
+        snakemake --lint
+        snakefmt workflow
+    - name: Integration dry-run test
+      run: |
+        snakemake -np
 
-  Testing:
-    runs-on: ubuntu-latest
-    needs: 
-      - Linting
-      - Formatting
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: Test workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .test
-        stagein: "pip install --no-deps -r .github/snakemake_action_requirements.txt"
-        snakefile: workflow/Snakefile
-        args: "--sdm apptainer --show-failed-logs --cores 1 --all-temp"
 
-    - name: Test report
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .test
-        stagein: "pip install --no-deps -r .github/snakemake_action_requirements.txt"
-        snakefile: workflow/Snakefile
-        args: "--report report.zip"
diff --git a/spimprep/__init__.py b/spimprep/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/workflow/Snakefile b/workflow/Snakefile
index d7d0f8c..57cf784 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -1,6 +1,6 @@
 import json
-from snakebids import bids, set_bids_spec
 from pathlib import Path
+from snakebids import bids, set_bids_spec
 import pandas as pd
 import os
 
@@ -9,13 +9,13 @@ configfile: "config/config.yml"
 
 
 container: config["containers"]["spimprep"]
-conda: config["conda_envs"]["global"]
+
 
 # use expandvars so we can use e.g. '$SLURM_TMPDIR'
 root = os.path.expandvars(config["root"])
 work = os.path.expandvars(config["work"])
 
-#this is needed to use the latest bids spec with the pre-release snakebids
+# this is needed to use the latest bids spec with the pre-release snakebids
 set_bids_spec("v0_10_1")
 
 # read datasets tsv
@@ -33,89 +33,7 @@ datasets = pd.read_csv(
 )
 
 
-def get_all_targets():
-    targets = []
-    for i in range(len(datasets)):
-        targets.extend(
-            expand(
-                bids(
-                    root=root,
-                    subject="{subject}",
-                    datatype="micr",
-                    sample="{sample}",
-                    acq="{acq}",
-                    desc="{desc}",
-                    stain="{stain}",
-                    suffix="spim.ome.zarr.zip",
-                ),
-                subject=datasets.loc[i, "subject"],
-                sample=datasets.loc[i, "sample"],
-                acq=datasets.loc[i, "acq"],
-                desc=config["targets"]["desc"],
-                stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
-            )
-        )
-        targets.extend(
-            expand(
-                bids(
-                    root=root,
-                    subject="{subject}",
-                    datatype="micr",
-                    sample="{sample}",
-                    acq="{acq}",
-                    desc="{desc}",
-                    from_="{template}",
-                    suffix="dseg.ome.zarr.zip",
-                ),
-                subject=datasets.loc[i, "subject"],
-                sample=datasets.loc[i, "sample"],
-                acq=datasets.loc[i, "acq"],
-                desc=config["targets"]["desc"],
-                template=config["templates"],
-                stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
-            )
-        )
-        targets.extend(
-            expand(
-                bids(
-                    root=root,
-                    subject="{subject}",
-                    datatype="micr",
-                    sample="{sample}",
-                    acq="{acq}",
-                    desc="{desc}",
-                    stain="{stain}",
-                    level="{level}",
-                    suffix="spim.nii",
-                ),
-                subject=datasets.loc[i, "subject"],
-                sample=datasets.loc[i, "sample"],
-                acq=datasets.loc[i, "acq"],
-                desc=config["targets"]["desc"],
-                level=config["nifti"]["levels"],
-                stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
-            )
-        )
-
-    return targets
-
-
-def get_dataset_path(wildcards):
-    df = datasets.query(
-        f"subject=='{wildcards.subject}' and sample=='{wildcards.sample}' and acq=='{wildcards.acq}'"
-    )
-    return df.dataset_path.to_list()[0]
-
-
-def get_stains(wildcards):
-    df = datasets.query(
-        f"subject=='{wildcards.subject}' and sample=='{wildcards.sample}' and acq=='{wildcards.acq}'"
-    )
-
-    return [
-        df.stain_0.to_list()[0],
-        df.stain_1.to_list()[0],
-    ]
+include: "rules/common.smk"
 
 
 rule all:
diff --git a/workflow/envs/global.yml b/workflow/envs/global.yml
deleted file mode 100644
index 698153c..0000000
--- a/workflow/envs/global.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-channels:
-  - nodefaults
-dependencies:
-  - pip:
-    - snakebids=0.10.2
-
diff --git a/workflow/rules/atlasreg.smk b/workflow/rules/atlasreg.smk
index 5124e8a..11a9766 100644
--- a/workflow/rules/atlasreg.smk
+++ b/workflow/rules/atlasreg.smk
@@ -1,7 +1,3 @@
-def bids_tpl(root, template, **entities):
-    """bids() wrapper for files in tpl-template folder"""
-    return str(Path(bids(root=root, tpl=template)) / bids(tpl=template, **entities))
-
 
 rule import_anat:
     input:
@@ -9,7 +5,12 @@ rule import_anat:
     output:
         anat=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
     log:
-        bids_tpl(root='logs',datatype="import_anat",template="{template}", suffix="log.txt")
+        bids_tpl(
+            root="logs",
+            datatype="import_anat",
+            template="{template}",
+            suffix="log.txt",
+        ),
     shell:
         "cp {input} {output}"
 
@@ -20,7 +21,12 @@ rule import_dseg:
     output:
         dseg=bids_tpl(root=root, template="{template}", suffix="dseg.nii.gz"),
     log:
-        bids_tpl(root='logs',datatype="import_dseg",template="{template}", suffix="log.txt")
+        bids_tpl(
+            root="logs",
+            datatype="import_dseg",
+            template="{template}",
+            suffix="log.txt",
+        ),
     shell:
         "cp {input} {output}"
 
@@ -31,7 +37,9 @@ rule import_lut:
     output:
         tsv=bids_tpl(root=root, template="{template}", suffix="dseg.tsv"),
     log:
-        bids_tpl(root='logs',datatype="import_lut",template="{template}", suffix="log.txt")
+        bids_tpl(
+            root="logs", datatype="import_lut", template="{template}", suffix="log.txt"
+        ),
     script:
         "../scripts/import_labelmapper_lut.py"
 
@@ -75,7 +83,7 @@ rule affine_reg:
         ),
     log:
         bids(
-            root='logs',
+            root="logs",
             subject="{subject}",
             datatype="affine_reg",
             sample="{sample}",
@@ -129,7 +137,7 @@ rule deform_reg:
         ),
     log:
         bids(
-            root='logs',
+            root="logs",
             subject="{subject}",
             datatype="deform_reg",
             sample="{sample}",
@@ -178,7 +186,7 @@ rule resample_labels_to_zarr:
         ),
     log:
         bids(
-            root='logs',
+            root="logs",
             subject="{subject}",
             datatype="resample_labels_to_zarr",
             sample="{sample}",
@@ -187,7 +195,6 @@ rule resample_labels_to_zarr:
             space="{template}",
             suffix="log.txt",
         ),
-
     script:
         "../scripts/resample_labels_to_zarr.py"
 
@@ -234,7 +241,7 @@ rule zarr_to_ome_zarr_labels:
         "preproc"
     log:
         bids(
-            root='logs',
+            root="logs",
             subject="{subject}",
             datatype="zarr_to_ome_zarr_labels",
             sample="{sample}",
diff --git a/workflow/rules/bigstitcher.smk b/workflow/rules/bigstitcher.smk
index 18847a2..2ed066a 100644
--- a/workflow/rules/bigstitcher.smk
+++ b/workflow/rules/bigstitcher.smk
@@ -11,7 +11,7 @@ rule zarr_to_bdv:
         ),
         metadata_json=rules.raw_to_metadata.output.metadata_json,
     params:
-        max_downsampling_layers=5,  #1,2,4,8,16
+        max_downsampling_layers=5,
         temp_h5=str(
             Path(
                 bids(
@@ -26,7 +26,6 @@ rule zarr_to_bdv:
             )
             / "dataset.h5"
         ),
-        #only temporary, is promptly deleted 
         temp_xml=str(
             Path(
                 bids(
@@ -41,7 +40,6 @@ rule zarr_to_bdv:
             )
             / "dataset.xml"
         ),
-        #only temporary, is promptly deleted 
     output:
         bdv_n5=temp(
             directory(
@@ -77,6 +75,16 @@ rule zarr_to_bdv:
             desc="{desc}",
             suffix="benchmark.tsv",
         )
+    log:
+        bids(
+            root="logs",
+            datatype="zarr_to_n5_bdv",
+            subject="{subject}",
+            sample="{sample}",
+            acq="{acq}",
+            desc="{desc}",
+            suffix="log.txt",
+        ),
     threads: 32
     group:
         "preproc"
@@ -86,29 +94,6 @@ rule zarr_to_bdv:
         "../scripts/zarr_to_n5_bdv.py"
 
 
-def get_fiji_launcher_cmd(wildcards, output, threads, resources):
-    launcher_opts_find = "-Xincgc"
-    launcher_opts_replace = f"-XX:+UseG1GC -verbose:gc -XX:+PrintGCDateStamps -XX:ActiveProcessorCount={threads}"
-    pipe_cmds = []
-    pipe_cmds.append("ImageJ-linux64 --dry-run --headless --console")
-    pipe_cmds.append(f"sed 's/{launcher_opts_find}/{launcher_opts_replace}'/")
-    pipe_cmds.append(
-        f"sed 's/-Xmx[0-9a-z]\+/-Xmx{resources.mem_mb}m -Xms{resources.mem_mb}m/'"
-    )
-    pipe_cmds.append("tr --delete '\\n'")
-    return "|".join(pipe_cmds) + f" > {output.launcher} && chmod a+x {output.launcher} "
-
-
-def get_macro_args_bigstitcher(wildcards, input, output):
-    return "{dataset_xml} {ds_x} {ds_y} {ds_z} {min_r}".format(
-        dataset_xml=input.dataset_xml,
-        ds_x=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_x"],
-        ds_y=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_y"],
-        ds_z=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_z"],
-        min_r=config["bigstitcher"]["filter_pairwise_shifts"]["min_r"],
-    )
-
-
 rule bigstitcher:
     input:
         dataset_n5=rules.zarr_to_bdv.output.bdv_n5,
@@ -164,7 +149,7 @@ rule bigstitcher:
     container:
         config["containers"]["spimprep"]
     resources:
-        runtime=30,  #this should be proportional to the number of images and image size
+        runtime=30,
         mem_mb=10000,
     threads: 32
     group:
@@ -176,21 +161,6 @@ rule bigstitcher:
         " && {output.launcher} &> {log} && {params.rm_old_xml}"
 
 
-def get_macro_args_zarr_fusion(wildcards, input, output):
-    return "{dataset_xml} {downsampling} {channel:02d} {output_zarr} {bsx} {bsy} {bsz} {bsfx} {bsfy} {bsfz}".format(
-        dataset_xml=input.dataset_xml,
-        downsampling=config["bigstitcher"]["fuse_dataset"]["downsampling"],
-        channel=get_stains(wildcards).index(wildcards.stain),
-        output_zarr=output.zarr,
-        bsx=config["bigstitcher"]["fuse_dataset"]["block_size_x"],
-        bsy=config["bigstitcher"]["fuse_dataset"]["block_size_y"],
-        bsz=config["bigstitcher"]["fuse_dataset"]["block_size_z"],
-        bsfx=config["bigstitcher"]["fuse_dataset"]["block_size_factor_x"],
-        bsfy=config["bigstitcher"]["fuse_dataset"]["block_size_factor_y"],
-        bsfz=config["bigstitcher"]["fuse_dataset"]["block_size_factor_z"],
-    )
-
-
 rule fuse_dataset:
     input:
         dataset_n5=bids(
@@ -299,7 +269,6 @@ rule fuse_dataset_spark:
             suffix="bigstitcher.xml",
         ),
         ijm=Path(workflow.basedir) / "macros" / "FuseImageMacroZarr.ijm",
-    params:
     output:
         zarr=temp(
             directory(
@@ -347,5 +316,3 @@ rule fuse_dataset_spark:
         "preproc"
     shell:
         "affine-fusion ..."
-
-
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
new file mode 100644
index 0000000..08623ba
--- /dev/null
+++ b/workflow/rules/common.smk
@@ -0,0 +1,157 @@
+# targets
+def get_all_targets():
+    targets = []
+    for i in range(len(datasets)):
+        targets.extend(
+            expand(
+                bids(
+                    root=root,
+                    subject="{subject}",
+                    datatype="micr",
+                    sample="{sample}",
+                    acq="{acq}",
+                    desc="{desc}",
+                    stain="{stain}",
+                    suffix="spim.ome.zarr.zip",
+                ),
+                subject=datasets.loc[i, "subject"],
+                sample=datasets.loc[i, "sample"],
+                acq=datasets.loc[i, "acq"],
+                desc=config["targets"]["desc"],
+                stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
+            )
+        )
+        targets.extend(
+            expand(
+                bids(
+                    root=root,
+                    subject="{subject}",
+                    datatype="micr",
+                    sample="{sample}",
+                    acq="{acq}",
+                    desc="{desc}",
+                    from_="{template}",
+                    suffix="dseg.ome.zarr.zip",
+                ),
+                subject=datasets.loc[i, "subject"],
+                sample=datasets.loc[i, "sample"],
+                acq=datasets.loc[i, "acq"],
+                desc=config["targets"]["desc"],
+                template=config["templates"],
+                stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
+            )
+        )
+        targets.extend(
+            expand(
+                bids(
+                    root=root,
+                    subject="{subject}",
+                    datatype="micr",
+                    sample="{sample}",
+                    acq="{acq}",
+                    desc="{desc}",
+                    stain="{stain}",
+                    level="{level}",
+                    suffix="spim.nii",
+                ),
+                subject=datasets.loc[i, "subject"],
+                sample=datasets.loc[i, "sample"],
+                acq=datasets.loc[i, "acq"],
+                desc=config["targets"]["desc"],
+                level=config["nifti"]["levels"],
+                stain=[datasets.loc[i, "stain_0"], datasets.loc[i, "stain_1"]],
+            )
+        )
+
+    return targets
+
+
+# import
+def cmd_get_dataset(wildcards, input, output):
+    cmds = []
+    import tarfile
+
+    # supports tar, tar.gz, tgz, zip, or folder name
+    dataset_path = Path(input.dataset_path)
+    suffix = dataset_path.suffix
+    if dataset_path.is_dir():
+        # we have a directory:
+        # return command to copy folder
+        cmds.append(f"ln -sr {input} {output}")
+
+    elif tarfile.is_tarfile(dataset_path):
+        # we have a tar file
+        # check if gzipped:
+        cmds.append(f"mkdir -p {output}")
+        if suffix == "gz" or suffix == "tgz":
+            cmds.append(f"tar -xzf {input} -C {output}")
+        else:
+            cmds.append(f"tar -xf {input} -C {output}")
+
+    else:
+        print(f"unsupported input: {dataset_path}")
+
+    return " && ".join(cmds)
+
+
+def get_dataset_path(wildcards):
+    df = datasets.query(
+        f"subject=='{wildcards.subject}' and sample=='{wildcards.sample}' and acq=='{wildcards.acq}'"
+    )
+    return df.dataset_path.to_list()[0]
+
+
+def get_stains(wildcards):
+    df = datasets.query(
+        f"subject=='{wildcards.subject}' and sample=='{wildcards.sample}' and acq=='{wildcards.acq}'"
+    )
+
+    return [
+        df.stain_0.to_list()[0],
+        df.stain_1.to_list()[0],
+    ]
+
+
+# bids
+def bids_tpl(root, template, **entities):
+    """bids() wrapper for files in tpl-template folder"""
+    return str(Path(bids(root=root, tpl=template)) / bids(tpl=template, **entities))
+
+
+# bigstitcher
+def get_fiji_launcher_cmd(wildcards, output, threads, resources):
+    launcher_opts_find = "-Xincgc"
+    launcher_opts_replace = f"-XX:+UseG1GC -verbose:gc -XX:+PrintGCDateStamps -XX:ActiveProcessorCount={threads}"
+    pipe_cmds = []
+    pipe_cmds.append("ImageJ-linux64 --dry-run --headless --console")
+    pipe_cmds.append(f"sed 's/{launcher_opts_find}/{launcher_opts_replace}'/")
+    pipe_cmds.append(
+        f"sed 's/-Xmx[0-9a-z]\+/-Xmx{resources.mem_mb}m -Xms{resources.mem_mb}m/'"
+    )
+    pipe_cmds.append("tr --delete '\\n'")
+    return "|".join(pipe_cmds) + f" > {output.launcher} && chmod a+x {output.launcher} "
+
+
+def get_macro_args_bigstitcher(wildcards, input, output):
+    return "{dataset_xml} {ds_x} {ds_y} {ds_z} {min_r}".format(
+        dataset_xml=input.dataset_xml,
+        ds_x=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_x"],
+        ds_y=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_y"],
+        ds_z=config["bigstitcher"]["calc_pairwise_shifts"]["downsample_in_z"],
+        min_r=config["bigstitcher"]["filter_pairwise_shifts"]["min_r"],
+    )
+
+
+def get_macro_args_zarr_fusion(wildcards, input, output):
+    return "{dataset_xml} {downsampling} {channel:02d} {output_zarr} {bsx} {bsy} {bsz} {bsfx} {bsfy} {bsfz}".format(
+        dataset_xml=input.dataset_xml,
+        downsampling=config["bigstitcher"]["fuse_dataset"]["downsampling"],
+        channel=get_stains(wildcards).index(wildcards.stain),
+        output_zarr=output.zarr,
+        bsx=config["bigstitcher"]["fuse_dataset"]["block_size_x"],
+        bsy=config["bigstitcher"]["fuse_dataset"]["block_size_y"],
+        bsz=config["bigstitcher"]["fuse_dataset"]["block_size_z"],
+        bsfx=config["bigstitcher"]["fuse_dataset"]["block_size_factor_x"],
+        bsfy=config["bigstitcher"]["fuse_dataset"]["block_size_factor_y"],
+        bsfz=config["bigstitcher"]["fuse_dataset"]["block_size_factor_z"],
+    )
diff --git a/workflow/rules/flatfield_corr.smk b/workflow/rules/flatfield_corr.smk
index 034b8e4..d5a9335 100644
--- a/workflow/rules/flatfield_corr.smk
+++ b/workflow/rules/flatfield_corr.smk
@@ -13,7 +13,7 @@ rule fit_basic_flatfield_corr:
         ),
     params:
         channel=lambda wildcards: get_stains(wildcards).index(wildcards.stain),
-        max_n_images=config["basic_flatfield_corr"]["max_n_images"],  #sets maximum number of images to use for fitting (selected randomly)
+        max_n_images=config["basic_flatfield_corr"]["max_n_images"],
         basic_opts=config["basic_flatfield_corr"]["fitting_opts"],
     output:
         model_dir=temp(
@@ -30,7 +30,7 @@ rule fit_basic_flatfield_corr:
             )
         ),
     resources:
-        runtime=90,  #this should be proportional to the number of images and image size
+        runtime=90,
         mem_mb=64000,
     threads: 8
     benchmark:
@@ -43,6 +43,16 @@ rule fit_basic_flatfield_corr:
             stain="{stain}",
             suffix="benchmark.tsv",
         )
+    log:
+        bids(
+            root="logs",
+            datatype="fit_basic_flatfield",
+            subject="{subject}",
+            sample="{sample}",
+            acq="{acq}",
+            stain="{stain}",
+            suffix="log.txt",
+        ),
     group:
         "preproc"
     container:
@@ -91,8 +101,17 @@ rule apply_basic_flatfield_corr:
             acq="{acq}",
             suffix="benchmark.tsv",
         )
+    log:
+        bids(
+            root="logs",
+            datatype="apply_basic_flatfield",
+            subject="{subject}",
+            sample="{sample}",
+            acq="{acq}",
+            suffix="log.txt",
+        ),
     resources:
-        runtime=60,  #this should be proportional to the number of images and image size
+        runtime=60,
         mem_mb=32000,
     threads: 32
     group:
diff --git a/workflow/rules/import.smk b/workflow/rules/import.smk
index 71ca961..bf552e2 100644
--- a/workflow/rules/import.smk
+++ b/workflow/rules/import.smk
@@ -1,29 +1,3 @@
-def cmd_get_dataset(wildcards, input, output):
-    cmds = []
-    import tarfile
-
-    # supports tar, tar.gz, tgz, zip, or folder name
-    dataset_path = Path(input.dataset_path)
-    suffix = dataset_path.suffix
-    if dataset_path.is_dir():
-        # we have a directory:
-        # return command to copy folder
-        cmds.append(f"ln -sr {input} {output}")
-
-    elif tarfile.is_tarfile(dataset_path):
-        # we have a tar file
-        # check if gzipped:
-        cmds.append(f"mkdir -p {output}")
-        if suffix == "gz" or suffix == "tgz":
-            cmds.append(f"tar -xzf {input} -C {output}")
-        else:
-            cmds.append(f"tar -xf {input} -C {output}")
-
-    else:
-        print(f"unsupported input: {dataset_path}")
-
-    return " && ".join(cmds)
-
 
 rule get_dataset:
     input:
@@ -46,6 +20,16 @@ rule get_dataset:
         ),
     group:
         "preproc"
+    log:
+        bids(
+            root="logs",
+            subject="{subject}",
+            datatype="get_dataset",
+            sample="{sample}",
+            acq="{acq}",
+            desc="raw",
+            suffix="log.txt",
+        ),
     shell:
         "{params.cmd}"
 
@@ -76,6 +60,15 @@ rule raw_to_metadata:
             acq="{acq}",
             suffix="benchmark.tsv",
         )
+    log:
+        bids(
+            root="logs",
+            datatype="raw_to_metdata",
+            subject="{subject}",
+            sample="{sample}",
+            acq="{acq}",
+            suffix="log.txt",
+        ),
     group:
         "preproc"
     container:
@@ -120,6 +113,15 @@ rule tif_to_zarr:
             acq="{acq}",
             suffix="benchmark.tsv",
         )
+    log:
+        bids(
+            root="logs",
+            datatype="tif_to_zarr",
+            subject="{subject}",
+            sample="{sample}",
+            acq="{acq}",
+            suffix="log.txt",
+        ),
     group:
         "preproc"
     threads: 32
diff --git a/workflow/rules/ome_zarr.smk b/workflow/rules/ome_zarr.smk
index e19717e..b403eb3 100644
--- a/workflow/rules/ome_zarr.smk
+++ b/workflow/rules/ome_zarr.smk
@@ -32,6 +32,17 @@ rule zarr_to_ome_zarr:
             )
         ),
     threads: 32
+    log:
+        bids(
+            root="logs",
+            subject="{subject}",
+            datatype="zarr_to_ome_zarr",
+            sample="{sample}",
+            acq="{acq}",
+            desc="{desc}",
+            stain="{stain}",
+            suffix="log.txt",
+        ),
     container:
         config["containers"]["spimprep"]
     group:
@@ -90,6 +101,18 @@ rule ome_zarr_to_nii:
             level="{level}",
             suffix="benchmark.tsv",
         )
+    log:
+        bids(
+            root="logs",
+            datatype="ome_zarr_to_nifti",
+            subject="{subject}",
+            sample="{sample}",
+            acq="{acq}",
+            desc="{desc}",
+            stain="{stain}",
+            level="{level}",
+            suffix="log.txt",
+        ),
     group:
         "preproc"
     threads: 32
@@ -97,25 +120,3 @@ rule ome_zarr_to_nii:
         config["containers"]["spimprep"]
     script:
         "../scripts/ome_zarr_to_nii.py"
-
-
-rule zarr_masking_wip:
-    input:
-        zarr=rules.zarr_to_ome_zarr.output.zarr,
-    output:
-        zarr=directory(
-            bids(
-                root=root,
-                subject="{subject}",
-                datatype="micr",
-                sample="{sample}",
-                acq="{acq}",
-                desc="{desc}",
-                stain="{stain}",
-                suffix="mask.ome.zarr",
-            )
-        ),
-    container:
-        config["containers"]["spimprep"]
-    notebook:
-        "../notebooks/zarr_masking.py.ipynb"