CODEWITHSUNDEEP
yamlsnakemake
user3224522
user3224522

Reputation: 1151

Snakemake merge multiples bam files using bamtools

I have several BAM files in different directories that I want to merge. In my config.yaml file I indicate the paths to the files I want to merge:

var:
   var1: [ "/DATA/utent3/DATI/var/var1/leaf/trimmed/leaf_var1_ref1.bam", "/DATA/utent3/DATI/var/var1/stem/trimmed/stem_var1_ref1.bam", "/DATA/utent3/DATI/var/var1/flower/trimmed/flower_var1_ref1.bam" ]
....
   var9: [ "/DATA/utent3/DATI/var/var9/leaf/trimmed/leaf_var9_ref1.bam", "/DATA/utent3/DATI/var/var9/stem/trimmed/stem_var9_ref1.bam", "/DATA/utent3/DATI/var/var9/flower/trimmed/flower_var9_ref1.bam" ]

executables:
    bamtools: /home/utent3/anaconda3/bin/bamtools

And this is my snakefile

configfile: "config.yaml"
workdir: "/DATA/utent3/DATI/var/"

rule all:
    input:
        expand("{sample}.accepted.bam", sample = config["var"])

rule bamtools:
    input:
        bams = lambda wildcards: config["var"][wildcards.sample]
    output:
        bam = "{sample}.accepted.bam"
    params:
        executable = config["executables"]["bamtools"]
    run:
        shell("{params.executable} merge -list {input.bams} -out {output.bam}")

I get this error:

WorkflowError: Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.

In general could someone explain how to write in config file multiple file paths.

UPDATE Now it says (for now I am trying only with var1):

ERROR: Some problems were encountered when parsing the command line options:
   An unrecognized argument was found: /DATA/utent3/DATI/var/var1/stem/trimmed/stem_var1_ref1.bam
   An unrecognized argument was found: /DATA/utent3/DATI/var/var1/flower/trimmed/flower_var1_ref1.bam

I think it is because it is not reading the config.file var correctly...

Upvotes: 0

Views: 177

Answers (2)

user3224522
user3224522

Reputation: 1151

So, according to bamtools help merge documentation, I solved the problem adjusting the following part of the script, for sure not the best way, but works:

run:
    shell("{params.executable} merge -in {input.bams[0]} -in {input.bams[1]} -in {input.bams[2]} -out {output.bam}")

Upvotes: 0

dariober
dariober

Reputation: 9062

I suspect you are executing snakemake as 

snakemake [opts] bamtools

instead of just 

snakemake [opts]

With the former command you are making "bamtools" the target rule which, as the error says, contains wildcards.

Upvotes: 1

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