Example for optional input in tuple?
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- 难度
- 3/5
- 预计耗时
- 1-2 天
- 新手友好度
- 30/100
- Issue 类型
- 缺陷
- 描述清晰度
- 基本清楚
- 活跃度
- 停滞
调研方向
Start with the tuple input declaration and the map expression in main.nf; the example reports Not a valid path value: NO_FILE when the optional reverse-read path is represented by that string. Check how this repository’s patterns handle optional tuple paths and compare with the Nextflow input documentation. Done means the example runs with and without an R2 file and publishes the expected BAM outputs.
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描述
I am trying to run a configuration where the input is a tuple of paths, some of which are optional. The pattern in this repository works for separate path inputs (or, so says the author), but extending it to my use case results in the error Not a valid path value: NO_FILE.
In this simple example demonstrating the issue, the input is a CSV file defining RNA-seq sample names, forward and reverse read fastqs, and a STAR genome index to align them to. The reverse read is optional.
My question to the community is how I can work around this issue.
Repository setup
nextflow.config
params {
manifest = null // csv file name,R1,R2?,index
outdir = "outs" // save output bams
}
profiles {
conda {
conda.enabled = true
process.conda = "star samtools"
}
}
main.nf
process MyProcess {
publishDir outdir, mode: "copy"
input:
tuple val(name), path(R1), path(R2), path(index)
path outdir
output:
path "${name}_Aligned.out.sortedByCoord.bam"
path "${name}_Aligned.out.sortedByCoord.bam.bai"
script:
R2_arg = R2.name == "NO_FILE" ? "" : R2
"""
STAR --readFilesIn $R1 $R2_arg --readFilesCommand gunzip -c \
--genomeDir $index --outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix ${name}_
samtools index ${name}_Aligned.out.sortedByCoord.bam
"""
}
workflow {
MyProcess(
file(manifest).read().splitCsv(header: ["name", "R1", "R2", "index"]).map{it.R2 = it.R2 ?: "NO_FILE"},
params.outdir
)
}
Run
nextflow run main.nf [-profile conda] --manifest path/to/manifest.csv
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