Hi snakemake doesn't seem to recognize my wildcards in my rule modkit. i defined all possible outputs and assigned to a list modkit_outputs. however, i get the error below and i'm not sure how to fix it. Building DAG of jobs... InputFunctionException in rule modkit in file //data1/greenbab/users/ahunos/apps/dorado_ont_wf/test_bedgraph.smk, line 29: Error: AttributeError: 'Wildcards' object has no attribute 'samples' Wildcards: Traceback: File "//data1/greenbab/users/ahunos/apps/dorado_ont_wf/test_bedgraph.smk", line 31, in <lambda> (rule modkit, line 40, //data1/greenbab/users/ahunos/apps/dorado_ont_wf/test_bedgraph.smk) parent_dir = "/data1/greenbab/users/ahunos/apps/dorado_ont_wf/" configfile: parent_dir + "config/config.yaml" configfile: "/data1/greenbab/users/ahunos/apps/dorado_ont_wf/config/samples_009TN_044TN.yaml" set_species = "human" #make sample list of bedgraphs motifs=["h", "m", "C"] strands=["positive", "negative"] minCoverages=[5, 10] samplesFromConfig=list(config["samples"].keys())#.tolist() print(f"{samplesFromConfig}") modkit_outputs = [ f"results/modkit/{sample}/{sample}_{motif}_CG0_{strand}.bedgraph" for sample in samplesFromConfig for motif in motifs for strand in strands ] print(f"modkit outputs\n {modkit_outputs}\n") rule all: input: modkit_outputs rule modkit: input: lambda wildcards: config["samples"][wildcards.samples] output: outputs=modkit_outputs priority: 100 params: reference_genome=lambda wildcards: config["mm10"] if set_species == "mouse" else config["hg38"], modkit_threads=16, modkit_prob_percentiles=0.1, outdir= "results/modkit/{samples}/" shell: """ modkit pileup --region chr17 --threads {params.modkit_threads} --bedgraph {input} {params.outdir} \ --prefix {wildcards.samples} --cpg --combine-mods --ref {params.reference_genome} """ Continue reading...