[Python] Snakemake WorkflowError: "Target rules may not contain wildcards" when using...

I’m trying to build a Snakemake pipeline that uses a checkpoint to dynamically determine {sequence} wildcards after processing patient data. My workflow structure is roughly:

A checkpoint dicom_to_nifti converts raw DICOM files for each {patient} into NIfTI files.

Then, for every {sequence} discovered inside each patient’s output folder, a downstream rule dummy_process_sequence processes that sequence.

Finally, I have a rule all that collects all final processed files via a Python function that inspects the checkpoint output.


import os

PATIENTS = [d for d in os.listdir("dataset/raw")]
print(f"Found {len(PATIENTS)} patients")

checkpoint dicom_to_nifti:
input: "raw/{patient}/"
output: directory("nifti/{patient}/")
conda: "envs/dicom_nifti_env.yaml"
shell: "python scripts/dicom_to_nifti.py {input} {output}"

rule dummy_process_sequence:
input: "nifti/{patient}/{sequence}.nii.gz"
output: "processed/{patient}/{sequence}.nii.gz"
shell:
"""
mkdir -p $(dirname {output})
echo "Processed {input}" > {output}
"""

def collect_outputs(wildcards):
files = []
for patient in PATIENTS:
ckpt_outdir = checkpoints.dicom_to_nifti.get(patient=patient).output[0]
for f in os.listdir(ckpt_outdir):
if f.endswith(".nii.gz"):
seq = f[:-7] # strip ".nii.gz"
files.append(f"processed/{patient}/{seq}.nii.gz")
return files

rule all:
input:
collect_outputs





When I run

snakemake --cores 1 -p

, I get the error:

WorkflowError:
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards at the command line, or have a rule without wildcards at the very top of your workflow (e.g. the typical "rule all" which just collects all results you want to generate in the end).
​

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