How to enable “output” to detect variables in “run” in snakemake
I am trying to make directories for the different “IDs” I have stored in the .csv file (they are stored under column “ID”). However, snakemake doesn’t seem to be able to detect “ID”
fastq-dump.3.1.1 err: item not found while constructing within virtual database module – the path ‘SRRXXXXX.sra’ cannot be opened as database or table
SRRs = [ “SRR11111111”, “SRR22222222”, “SRR33333333”, “SRR44444444”, “SRR55555555”, “SRR66666666”, “SRR77777777” ] rule all: input: expand(“../atac_seq/{srr}/{srr}_1.fastq.gz”, srr=SRRs), expand(“../atac_seq/{srr}/{srr}_2.fastq.gz”, srr=SRRs), expand(“../atac_seq/{srr}/{srr}_3.fastq.gz”, srr=SRRs), expand(“../atac_seq/{srr}/{srr}_4.fastq.gz”, srr=SRRs) rule fastq_dump: output: “../atac_seq/{n}/{n}_1.fastq.gz”, “../atac_seq/{n}/{n}_2.fastq.gz”, “../atac_seq/{n}/{n}_3.fastq.gz”, “../atac_seq/{n}/{n}_4.fastq.gz” shell: “”” fastq-dump –split-files –gzip {wildcards.n}.sra “”” Hi all, right now in the directory /atac_seq/{srr}/ there is only a .sra file. I want to expand the […]
Snakemake how to move files created to a new directory of same name
Some code taken from: Snakemake – How do I use each line of a file as an input?