downloading fastq from snakemake

Question

I am trying desperately to have a rule downloading my fastq files before executing the following rules. I tried a lot of things including what is suggested here: http://ivory.idyll.org/blog/tag/snakemake.html

Below is a simplified version of my snakemake:

######### functions

def read_samplesTable(inputTable):
    data = pandas.read_csv(inputTable)
    # Verify column names
    if not {'run', 'organism', 'name', 'experiment_title', 'cell_line', 'rep', 'study_name', 'library_strategy', 'library_layout', 'study_title'}.issubset(data.columns.values):
            raise KeyError("The samples file must contain the following named columns: 'run', 'organism', 'name', 'experiment_title', 'cell_line', 'rep', 'study_name', 'library_strategy', 'library_layout', 'study_title'")
    return data

def retrieveName(description):
    result = []
    for items in description.iteritems():
        result.append(items[1].split(":")[0])
    return result 

######### Variables

input_table = config["samples"]["summaryFile"]
samplesData = read_samplesTable(input_table)

index_single = samplesData['library_layout'] == 'SINGLE - '
samplesData_single = samplesData[index_single]

gsm_single = retrieveName(samplesData_single["experiment_title"])
outputName_single = samplesData_single['name'] + "_" + samplesData_single['run'] + "_" + gsm_single + "_" + samplesData_single['study_name'] + "_" + samplesData_single['cell_line'] + "_" + samplesData_single['rep']
single_samples = outputName_single.tolist()

names_srrID_single = samplesData_single['run']

############ Rule

rule all:
  input:
    expand("data/single/{singleEndName}.fastq.gz", singleEndName = single_samples)

rule download_fastq_single:
  output:
    singleFastq = "data/single/{singleEndName}.fastq.gz"
  params:
    outputdirectory = config["rawdata"]["fastqrootfolder"]
    ssridsingle = lambda wildcards: samplesData_single.loc[wildcards.names_srrID_single, "run"]    
  shell:
    "fastq-dump --accession {params.srridsingle} --defline-seq '@$sn[_$rn]/$ri' --defline-qual \'+\' --gzip --outdir {params.outputdirectory}"

The rule is in a separate file 'download-fastq-snakefile' and I get the error SyntaxError in line 6 of download-fastq-snakefile.

The problem, as I expected, is coming from the line ssridsingle = lambda wildcards: samplesData_single.loc[wildcards.names_srrID_single, "run"]

If you could help me that would be fantastic!

Thanks

Answer 1

My guess the problem is simply a missing comma:

  params:
    outputdirectory = config["rawdata"]["fastqrootfolder"], <-- add this comma
    ssridsingle = lambda wildcards: samplesData_single.loc[wildcards.names_srrID_single, "run"]