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Results tagged with nextflow
Search options questions only
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user 3839
1
vote
1
answer
1k
views
Nextflow: ordering the execution of processes; outputs of process A are inputs of process B
A_some_ch
val (some other val), path(some other path) from A_some_other_ch
output:
some val and path
script:
"""
some commands out some files
"""
}
I got the idea using of flag from here: https://github.com/nextflow-io …
- 317
1
vote
1
answer
1k
views
Nextflow error: can not invoke method minus () on null object
Hi I was trying to use plink in nextflow and getting the error mentioned in the subject. Here is my code, any help what I am missing. … I am new in nextflow, it was ok when input was a single file, but for grouped files, I am getting lost.
params.dir='data/'
params.publish="output/"
Channel
.fromFilePairs("${params.dir}*. …
- 317
2
votes
1
answer
426
views
Input from multiple channel, merge and use in nextflow
I need to merge multiple channel to reuse them in two processes. So far I tried as follows:
channel.from([15,20,21]).into {k1;k2}
channel.from(['a','b','c']).into {m1;m2}
channel.from([1,2,3]).into {l …
- 317
3
votes
1
answer
818
views
splitCsv map with text, join with another channel, nextflow
I have a csv file which describes number of chunks per chromosome, like;
chrom,chunks
chr1,"CHUNKS=([1]=""0e6 3e6"" [2]=....)"
chr2,"CHUNKS=([1]=""0e6 3e6"" [2]=....)"
chr3,"CHUNKS=([1]=""0e6 3e6"" [2 …
- 317
2
votes
1
answer
2k
views
Nextflow: run sbatch (slurm job script) inside a process
For instance, I have a job script 'PRE_PHASING_QC.JOB' and outside nextflow it runs perfectly, I want to integrate it in a nextflow script. … I guess that I have to declare outputs inside nextflow process. …
- 317
2
votes
1
answer
3k
views
Merge multiple channels each emits multiple files in nextflow
I need to merge multiple channels each emits multiple file. So far I did something as below:
process prephasing {
publishDir params.out, mode:'copy'
input:
tuple val(prefix), path(bfiles) from plink_d …
- 317
0
votes
0
answers
621
views
parse csv/text file to create a channel with array in nextflow
How could I read a csv/text file in nextflow?
Suppose, I have above csv file with 3 columns. … Sorry, I could not provide any nextflow script that I tried, because I not sure how create an array with splitCsv
I have tried in python:
df1=pd.read_csv('data1/omni-ec-eur-fin-pass-qc.bim',sep='\t',header …
- 317
0
votes
1
answer
828
views
nextflow: Filter outputs of a process
How could I filter outputs of a process in the input of the next process? Filtering works fine in channel, but if I try to filter outputs I got compilation error. I tried as follows:
Channel
.fromFile …
- 317
3
votes
1
answer
1k
views
Nextflow: No signature of Method: chr() is applicable for argument types; unknown variable
I was trying to use plink in nextflow. My first process will split the input (single bed|bim|fam file) into 22 chromosomes (each with bed|bim|fam files) which would be used in subsequent processes. …
- 317
2
votes
1
answer
629
views
Nextflow: Runs without error, produce few but not all output files into output channel
I was trying to develop a pipeline using nextflow and plink. My code runs without any error, but got only two output files instead of 22 (one for each chromosome). …
- 317