I'm attempting to run a nextflow pipeline and have begun getting unexpected output for a few of the processes in my pipeline. I believe this to be a syntax error, but I am not sure where to correct it. Any help is finding where my error is located is appreciated.
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
import groovy.io.*
process hisat2Alignment {
fastq1 = NS.1389.002.NEBNext_dual_i7_*_R1.fastq.gz
fastq2 = NS.1389.002.NEBNext_dual_i7_*_R2.fastq.gz
input:
tuple path("fastq1"), path("fastq2")
output:
tuple path("*.sam"), val(fastq1.baseName.substring(0, fastq1.baseName.indexOf("_R1")))
script:
"""
hisat2 -p 16 -x genome -1 ${fastq1} -2 ${fastq2} -S mapped_${baseName}.sam
"""
}
process Stringtier {
publishDir "${params.baseDir}/assembled/$baseName", mode: "move"
env {
PATH = $PATH:/data/selena/stringtie-2.2.1
}
input:
tuple path(mapped_bam), val(baseName)
output:
tuple path("*.gtf"), val(baseName)
script:
"""
stringtie -e -G ${params.annotation} -o ${baseName}.gtf ${mapped_bam}
"""
}
workflow {
samples = new File(params.configFilePath).readLines()*.split('\t');
samples = Channel.fromList(samples);
hisat2Alignment(samples);
assembled = Stringtier(samples)
}
