https://bioinformaticsonline.com/snippets/view/41412/download-with-snakemake? https://bioinformaticsonline.com/snippets/view/41412/download-with-snakemake Wed, 11 Mar 2020 07:16:44 -0500 https://bioinformaticsonline.com/snippets/view/41412/download-with-snakemake # list sample names & download URLs. sample_links = {"ERR458493": "https://osf.io/5daup/download", "ERR458494":"https://osf.io/8rvh5/download", "ERR458495":"https://osf.io/2wvn3/download", "ERR458500":"https://osf.io/xju4a/download", "ERR458501": "https://osf.io/nmqe6/download", "ERR458502": "https://osf.io/qfsze/download"} # the sample names are dictionary keys in sample_links. extract them to a list we can use below SAMPLES=sample_links.keys() # download yeast rna-seq data from Schurch et al, 2016 study rule download_all: input: expand("rnaseq/raw_data/{sample}.fq.gz", sample=SAMPLES) # rule to download each individual file specified in sample_links rule download_reads: output: "rnaseq/raw_data/{sample}.fq.gz" params: # dynamically generate the download link directly from the dictionary download_link = lambda wildcards: sample_links[wildcards.sample] shell: """ curl -L {params.download_link} -o {output} """]]> Surabhi Chaudhary