Comments (1)
Ah ok, I think now I understand what you meant in #8. But still, in a normal use case people will have either single-end or paired-end reads and assemble the set with different tools. So the input should be not single- and paired-end reads at one time. Allowing both types as a mixed input complicates everything I guess.
Here some example code for CSV input that might help as a starting point:
// illumina reads input & --list support
if (params.illumina && params.list) { illumina_input_ch = Channel
.fromPath( params.illumina, checkIfExists: true )
.splitCsv()
.map { row -> ["${row[0]}", [file("${row[1]}", checkIfExists: true), file("${row[2]}", checkIfExists: true)]] }
.view() }
else if (params.illumina) { illumina_input_ch = Channel
.fromFilePairs( params.illumina , checkIfExists: true )
.view() }
In this case, FASTQ files are provided to the params.illumina
parameter and if additionally params.list == true
a CSV is expected instead of the FASTQs directly.
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Related Issues (10)
- Add conda support HOT 1
- rnaQUAST docker HOT 3
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- Paired-end read support HOT 5
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