How to download a list of `FastQ` files in `Nextflow` using `fromSRA` function? - bioinformatics

Question

I have a tsv file with various columns. One of the columns of interest for me is the run_accession column. It contains accession id of various genome data samples. I want to write a pipeline in Nextflow which reads accession ids from this file using the following command:
cut -f4 datalist.tsv | sed -n 2,11p
Output:
ERR2512385
ERR2512386
ERR2512387
ERR2512388
ERR2512389
ERR2512390
ERR2512391
ERR2512392
ERR2512393
ERR2512394
and feed this list of IDs into Channel.fromSRA method. So far, I have tried this:
#!/home/someuser/bin nextflow
nextflow.enable.dsl=2
params.datalist = "$baseDir/datalist.tsv"
process fetchRunAccession {
input:
path dlist
output:
file accessions
"""
cut -f4 $dlist | sed -n 2,11p
"""
}
process displayResult {
input:
file accessions
output:
stdout
"""
echo "$accessions"
"""
}
workflow {
accessions_p = fetchRunAccession(params.datalist)
result = displayResult(accessions_p)
result.view { it }
}
And I get this error:
Error executing process > 'fetchRunAccession'
Caused by:
Missing output file(s) `accessions` expected by process `fetchRunAccession
If I run just the first process it works well and prints 10 lines as expected. The second process is just a placeholder for the actual fromSRA implementation but I have not been able to use the output of first process as the input of second. I am very new to Nextflow and my code probably has some silly mistakes. I would appreciate any help in this matter.

Answer 1

The fromSRA function is actually a factory method. It requires either a project/study id, or one or more accession numbers, which must be specified as a list. A channel emitting accession numbers (like in your example code) will not work here. Also, it would be better to avoid spawning a separate job/process just to parse a small CSV file. Instead, just let your main Nextflow process do this. There's lots of ways to do this, but for CSV input I find using Nextflow's CsvSplitter class makes this easy:
import nextflow.splitter.CsvSplitter
nextflow.enable.dsl=2
def fetchRunAccessions( tsv ) {
def splitter = new CsvSplitter().options( header:true, sep:'\t' )
def reader = new BufferedReader( new FileReader( tsv ) )
splitter.parseHeader( reader )
List<String> run_accessions = []
Map<String,String> row
while( row = splitter.fetchRecord( reader ) ) {
run_accessions.add( row['run_accession'] )
}
return run_accessions
}
workflow {
accessions = fetchRunAccessions( params.filereport )
Channel
.fromSRA( accessions )
.view()
}
Note that Nextflow's ENA download URL was updated recently. You'll need the latest version of Nextflow (21.07.0-edge) to get this to run easily:
NXF_VER=21.07.0-edge nextflow run test.nf --filereport filereport.tsv