This is the code I have written till mapping. It works fine till the trimming part as it takes 1 input. But throws an error while mapping. Please help in finding where I went wrong.
//rna_script.nf
nextflow.enable.dsl=2
/*
* pipeline input parameters
*/
params.reads = "/home/user2/rnatoy/data/ggal/*.fq"
params.genome = "/home/user2/rnatoy/data/ggal/ggal_1_genome.fa"
params.outdir = 'results'
log.info """\
R N A P I P E L I N E
=============================
genome: ${params.genome}
reads : ${params.reads}
outdir: ${params.outdir}
"""
.stripIndent()
/*
* Step 1. QUALITY CHECK
*/
process QUALITY {
input :
path( params.reads)
script:
"""
fastqc ${params.reads} -o /home/user2/Dock/results
"""
}
/*
* Step 2.TRIM
*/
process TRIM {
input :
path params.reads
output :
path '*trimmed.fq', emit : trimmed
script:
"""
trim_galore ${params.reads} -o /home/user2/Dock/results/TRIMMED/trimmed.fq
"""
}
/*
* Step 3. Builds the genome index required by the mapping process
*/
process buildIndex {
input:
path params.genome
output:
path 'genome.index*', emit : index
"""
bowtie2-build --threads $task.cpus ${params.genome} genome.index
"""
}
/*
* Step 3. ALIGNMENT
*/
process mapping {
input:
path TRIM.out
path buildIndex.out
output:
path "accepted_hits.sam"
"""
bowtie2 -x buildIndex.out ${trimmed} -S accepted_hits.sam
"""
}
workflow {
buildIndex(Channel.fromPath( params.genome ) )
QUALITY(Channel.fromPath( params.reads ) )
TRIM(Channel.fromPath( params.reads ) )
mapping(Channel.fromPath(TRIM.out, buildIndex.out ))
}
•
written
by
Srinka •
3 answers
there is not output named "out" for TRIM. It's named "trimmed"
path '*trimmed.fq', emit : trimmed
you want something like: TRIM.trimmed
Unless you want to have some custom code, I suggest you start with https://nf-co.re/rnaseq
yes, you are right. If you want to learn it you should write it yourself. If it is a one-off thing that you have to do it quickly (as in industry), go to the dockerized workflow is the right choice.
Paths in nextflow I see you are trying to output nextflow data to a hard coded path when trimming - don't to this, it will cause major problems, so let Nextflow handle input and output directories and paths for you as much as possible.
trim_galore ${params.reads} -o /home/user2/Dock/results/TRIMMED/trimmed.fq
So just do something like this
trim_galore ${params.reads} -o trimmed.fq
I would also learn how to put your reads in an input channel instead of passing ${params.reads} around everywhere. See great examples here:
Thank you so much for this help but another error is thrown as shown in the picture -
The workflow was given as -
workflow {
mapping(Channel.fromPath('TRIM.out', 'buildIndex.out'))
}
The process is written as -
process mapping {
input:
path 'TRIM.out'
path 'buildIndex.out'
"""
bowtie2 -x $buildIndex.out $TRIM.out -S accepted_hits.sam
"""
}
•
written
by
Srinka •
Have a look at the complete Nextflow examples for RNA-seq - these deal with multiple inputs and outputs, which is the problem here.
https://github.com/CRG-CNAG/CalliNGS-NF/blob/master/modules.nf
workflow {
mapping(Channel.fromPath('TRIM.out', 'buildIndex.out'))
}
// I write my processes like this:
process mapping {
input:
file trimmed_R1 // just try with Read1 until you get the hang of how it works, Read2 will complicate the pipeline
file index // this will only input 1 file called index, which is not sufficient as indices are mostly 6+ files
"""
bowtie2 -x $index $trimmed_R1 -S accepted_hits.sam
"""
}
Sorry, not sure what you mean. I think it's worth looking at a lot of entry level Nextflow stuff to pass 1 file input and 1 file output through a workflow using Nextflow DSL2. Nothing fancy, just to gain experience. Or take an RNA-seq pipeline like the output I suggested, break it, and repair it - googling the error messages to get more experience. The Nextflow docs are pretty good and they provide lots of examples.
Here is a youtube video of an RNA-seq pipeline being built in nf -
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this is really wrong.
trim_galore should use the
inputfrom its ownprocessand the output shouldn't be a full path.