I have a target rule and a Trimmomatic rule, when I run my snakefile it completes after the target rule. I'm not sure what else I need to do. My Trimmomatic shell script works when I run it by itself and I don't see any obvious mistakes in my configuration files. I would appreciate some assistance.

Step 1: QC-pathway to trimmomatic_pe configuration file: short reads quality control

JSON does not support comments: Parameters for trimmomatic in config.json file

configfile: "/Users/shaedeycool/mambaforge/SMM_MSc_pipeline/config.json"

Step 2: Specify samples

f is a list

samples = {f[:] for f in os.listdir(".") if f.endswith(".fastq.gz")}

Step 3: Need a Master rule that requires all of your desired outputs as inputs

rule all: input: paired=expand("/metagenomics/{sample}.paired.fastq.gz", sample=samples), unpaired=expand("/metagenomics/{sample}.unpaired.fastq.gz", sample=samples)

Step 5: Metagenomic Illumina short reads quality control (Trimmomatic) for megaSPAdes assembly

rule trimmomatic_qc: input: forward = "/metagenomics/{sample}_R1_001.fastq.gz", reversed = "/metagenomics/{sample}_R2_001.fastq.gz" output: forward_paired = "/metagenomics/{sample}.paired.fastq.gz", forward_unpaired = "/metagenomics/{sample}.unpaired.fastq.gz", reversed_paired = "/metagenomics/{sample}_R2_001.paired.fastq.gz", reversed_unpaired = "/metagenomics/{sample}_R2_001.unpaired.fastq.gz" conda: "/Users/shaedeycool/mambaforge/envs/trim_pe.yaml" log: "logs/trimmomatic/{sample}.log" script: "/Users/shaedeycool/mambaforge/SMM_MSc_pipeline/trimmomatic_pe.sh"