snakemake

I am trying to run a simple one-rule snakemake file as following: resources_dir='resources' rule downloadReference: output: fa = resources_dir+'/human_g1k_v37.fasta', fai = resources_dir+'/human_g1k_v37.fasta.fai', shell: ('mkdir -p '+resources_dir+'; cd '+resources_dir+'; ' + 'wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz; gunzip human_g1k_v37.fasta.gz; ' + 'wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.fai;') But I get an error as : Error in job downloadReference while creating output files resources

I would like to be able to have my snakemake workflows continue running even when certain rules fail. For example, I'm using a variety of tools in order to perform peak-calling of ChIP-seq data. However, certain programs issue an error when they are not able to identify peaks. I would prefer to create an empty output file in such cases, and not having snakemake fail (like some peak-callers already do). Is there a snakemake-like way of handling such cases, using the "shell" and "run" keywords? Thanks For shell commands, you can always take advantage conditional "or", || : rule some_rule: output

I have a problem figuring out how to make the input directive only select all {samples} files in the rule below. rule MarkDup: input: expand("Outputs/MergeBamAlignment/{samples}_{lanes}_{flowcells}.merged.bam", zip, samples=samples['sample'], lanes=samples['lane'], flowcells=samples['flowcell']), output: bam = "Outputs/MarkDuplicates/{samples}_markedDuplicates.bam", metrics = "Outputs/MarkDuplicates/{samples}_markedDuplicates.metrics", shell: "gatk --java-options -Djava.io.tempdir=`pwd`/tmp \ MarkDuplicates \ $(echo ' {input}' | sed 's/ / --INPUT /g') \ -O {output.bam} \ --VALIDATION

Sorry if this is a naive question, but I'm still trying to wrap my head around the intricacies of Snakemake. I have a directory containing a number of files that I want to apply a rule to in parallel (i.e. I want to submit the same script to the cluster, specifying a different input file for each submission). I first tried using expand for the input files, but this only resulted in one job submission: CHROMS = [str(c) for c in range(1, 23)] + ["X"] rule vep: input: expand("data/split/chr{chrom}.vcf", chrom=CHROMS) output: expand("data/vep/split/chr{chrom}.ann.vcf", chrom=CHROMS) shell: "vep "

Can anybody help me understand if it is possible to access sample details from a config.yml file when the sample names are not written in the snakemake workflow? This is so I can re-use the workflow for different projects and only adjust the config file. Let me give you an example: I have four samples that belong together and should be analyzed together. They are called sample1-4. Every sample comes with some more information but to keep it simple here lets say its just a name tag such as S1, S2, etc. My config.yml file could look like this: samples: ["sample1","sample2","sample3","sample4"]

I'm trying to first generate 4 files, for the LETTERS x NUMS combinations, then summarize over the NUMS to obtain one file per element in LETTERS: LETTERS = ["A", "B"] NUMS = ["1", "2"] rule all: input: expand("combined_{letter}.txt", letter=LETTERS) rule generate_text: output: "text_{letter}_{num}.txt" shell: """ echo "test" > {output} """ rule combine text: input: expand("text_{letter}_{num}.txt", num=NUMS) output: "combined_{letter}.txt" shell: """ cat {input} > {output} """ Executing this snakefile results in the following error: WildcardError in line 19 of /tmp/Snakefile: No values given