I have a snakemake rule like: rule get_coverage: input: cram=lambda wildcards: expand(config[‘input’][‘cram’][wildcards.reference_genome], #access_id = access_id[wildcards.sample_name], sample_name='{sample_name}’), bai=lambda wildcards: expand(config[‘input’][‘cram’][wildcards.reference_genome] + ‘.crai’, #access_id = access_id[wildcards.sample_name], sample_name='{sample_name}’), ref=lambda wildcards: config[‘reference_genome’][wildcards.reference_genome], chrom_size=lambda wildcards: config[‘chrom_size’][wildcards.reference_genome] output: coverage=directory(config[‘output’][‘median_coverage’]) conda: src + ‘/env/acc_mask.yml’ threads: 19 script: """ mosdepth \ -n \ -t {threads} \ –use-median \ -f {input.ref} \ -b {input.chrom_size}… Read More snakemake threads wildcards not found

I have a snakemake srcipt like # minimal example configfile: "../snakemake/config.yaml" import os rule generateInclude: input: archaic_inc=config[‘input’][‘archaic_include’], modern_inc=config[‘input’][‘modern_include’] output: all_include=’include_{reference_genome}.bed’ params: reference_genome='{reference_genome}’ shell: """ if [ {params.reference_genome}==’hg19′ ]; then bedtools intersect -a <(zcat {input.archaic_inc} | sed ‘s/^chr//’) \ -b <(zcat {input.modern_inc} | sed ‘s/^chr//’) > {output.all_include} else bedtools intersect -a <(zcat {input.archaic_inc}) \ -b <(zcat… Read More Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards error

I have a snakemake pipeline where I need to do a small step of processing the data (applying a rolling average to a dataframe). I would like to write something like this: rule average_df: input: # script = , df_raw = "{sample}_raw.csv" params: window = 83 output: df_avg = "{sample}_avg.csv" shell: """ python import pandas… Read More Run short python code directly on snakemake

I can find examples of yaml config files, but I can’t find any json config files, and my guesses are failing How do I do this in a JSON config file, such that config["samples"] will return the correct values? Yaml: samples: A: data/samples/A.fastq B: data/samples/B.fastq >Solution : If you have config.yaml that looks like this:… Read More What is the format for a Snakemake JSON config file?