snakemake program not running all functions?

Sushil Shakyawar 0
Viewed 23
configfile: "config.yaml"
DATA = config['DATA_DIR']
BIN = config['BIN']
JASPAR = config['DATA_DIR']
RESULTS = config['RESULTS']
# JASPAR = "{0}/JASPAR2020".format(DATA)
JASPARS, ASSEMBLIES, BATCHES, TFS, BEDS = glob_wildcards(os.path.join(DATA, "{jaspar}", "{assembly}", "TFs", "{batch}", "{tf}", "{bed}.bed"))
rule all:
input:
    expand (os.path.join(RESULTS, "{jaspar}", "{assembly}", "LOLA_dbs", "JASPAR2020_LOLA_{batch}.RDS"), jaspar = JASPARS, assembly = ASSEMBLIES, batch = BATCHES)

rule createdb:
input:
    files = expand(os.path.join(RESULTS, "{jaspar}", "{assembly}", "data", "{batch}", "{tf}", "regions", "{bed}.bed"), zip, jaspar = JASPARS, assembly = ASSEMBLIES, batch = BATCHES, tf = TFS, bed = BEDS)
output:
    os.path.join(RESULTS, "{jaspar}", "{assembly}", "LOLA_dbs", "JASPAR2020_LOLA_{batch}.RDS")
    
shell:
    """
    R --vanilla --slave --silent -f {BIN}/create_lola_db.R \
    --args {RESULTS}/{wildcards.jaspar}/{wildcards.assembly}/data/{wildcards.batch} \
    {output};
    """

Why my snakemake program is not considering "createdb" rule. It is only considering "all". Can someone please help me with this?

snakemake shell
1 Answers

"snakemake only runs the first rule in a Snakefile, by default." - SOURCE

If that first rule's input isn't clearly linked to createdb, it's not going to know to run createdb. Because the only rule it wants to run would have to depend on createdb.

I suspect your problem is the input to your rule createdb shouldn't have expand() used for all the wildcards already handled by rule all, just bed?. See here.
Also other avenues to consider for debugging is investigating what you unpacked glob_wildcards() to and what files is.

userulHz0
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