Rscript use with snakemake - The rule is not executed

Question

[regue.hadrien]

Hi there!

I'm trying to build my first snakemake pipeline. I want to create a rule which can split a csv file into many. Each time I get a "Nothing to be done." message. Thus, it seems my rule is simply not executed, and I cant solve the problem.

Here is my first rule which is working properly:

rule xls_to_fasta_csv:
input:
    xls_file = "data/last_gisaid_xls.xls"
output:
    metadata_raw = "temp_data/metadata_raw.csv",
    fasta_seq = "temp_data/sequences.fasta"      
shell:
    "script/process_xls.py {input} {output.fasta_seq} {output.metadata_raw}"

And there is the non-executing rule:

rule make_metadata:
input:
    csv_file = rules.xls_to_fasta_csv.output.metadata_raw,
    script = "script/make_metadata.R"
output:
    H1N1_S4 = "temp_data/H1N1_S4.tsv",
    H1N1_S6 = "temp_data/H1N1_S6.tsv",
    H3N2_S4 = "temp_data/H3N2_S4.tsv",
    H3N2_S6 = "temp_data/H3N2_S6.tsv",
    B_S4 = "temp_data/B_S4.tsv",
    B_S6 = "temp_data/B_S6.tsv"
script:
    "{input.script} {input.csv_file}"
    "{output.H1N1_S4} {output.H1N1_S6k}"
    "{output.H3N2_S4} {output.H3N2_S6}"
    "{output.B_S4} {output.B_S6}"

At last, here is the first and last lines of my R script:

raw_metadata<-snakemake@input[[1]]
H1N1_S4_output<-snakemake@output[[1]]
H1N1_S6_output<-snakemake@output[[2]]
H3N2_S4_output<-snakemake@output[[3]]
H3N2_S4_output<-snakemake@output[[4]]
B_S4_output<-snakemake@output[[5]]
B_S4_output<-snakemake@output[[6]]
#some code
write.table(H1N1_S4,file=H1N1_S4,col.names = TRUE,row.names = FALSE,quote=FALSE,sep="\t")
write.table(H1N1_S6,file=H1N1_S6,col.names = TRUE,row.names = FALSE,quote=FALSE,sep="\t")
write.table(H3N2_S4,file=H3N2_S4,col.names = TRUE,row.names = FALSE,quote=FALSE,sep="\t")
write.table(H3N2_S6,file=H3N2_S6,col.names = TRUE,row.names = FALSE,quote=FALSE,sep="\t")
write.table(B_S4,file=B_S4,col.names = TRUE,row.names = FALSE,quote=FALSE,sep="\t")
write.table(B_S6,file=B_S6,col.names = TRUE,row.names = FALSE,quote=FALSE,sep="\t")

It's probably not the regular way to use R with snakemake, so I take any advice. thank:)

[Devon Ryan]

Do you have an all rule or something like that at the beginning? You would normally put all of your final output files there. The message from snakeMake has nothing to do with your R script, since it's not even being run.

[regue.hadrien]

I've added a rule:

rule all:
    input:
        xls_file = "data/last_gisaid_xls.xls"
    output:
        H1N1_S4 = "temp_data/H1N1_S4.tsv",
        H1N1_S6 = "temp_data/H1N1_S6.tsv",
        H3N2_S4 = "temp_data/H3N2_S4.tsv",
        H3N2_S6 = "temp_data/H3N2_S6.tsv",
        B_S4 = "temp_data/B_S4.tsv",
        B_S6 = "temp_data/B_S6.tsv"

Now the first rule xls_to_fasta_csv is not executed to, only the all rule, and of course, it fail. Any clues?

[Devon Ryan]

remove the output section, those files should all be in the input.

[regue.hadrien]

Well thank you, it work perfectly now:)

Last question: if I want to add more rules, I have to upgrade the all rule with the final files, or simply add them in the input section?

Thx again!

[Devon Ryan]

all should have all final files that you want from all of your rules. Generally you'll add various rules with intermediate files, which then don't need to be added to the all rule.

BTW, if you ever need to use make and makefiles, you'll see that snakeMake is modeled after them, since this is also how they work.