Questions tagged [nextflow]

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2answers
62 views

How do I call variants using BCFTools without piping mpileup file?

I need to call variants on a large number of reads using both VarScan2 and BCFTools. Both of these variant calling tools use <...
1
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1answer
63 views

Why are my Nextflow processes not executing in parallel?

I have written a Nextflow script with three process: The first process takes a pair of fastq files and aligns with reference genome. The process writes the ...
1
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1answer
62 views

Nextflow: How to initialize channel from CSV file but only after CSV file created?

Process A runs a python script which generates a CSV file in some absolute file path say "/mnt/x/blah.csv". Process B needs to consume the CSV file line by line, after process A has finished....
2
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1answer
59 views

use same output in two processes in nextflow dsl2

This is my workflow: ...
2
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0answers
57 views

How to execute several processes sequentially, without channels?

Using DSL2. I have processes A, B, C which I want to run in sequence - B waits for A to finish, C waits for B to finish. They are not communicating via channels so I can't do A.out.collect(). I have ...
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0answers
48 views

Nextflow: Why does non-local reference to $projectDir break hash stability and hence break task cache?

I have a process like the following: ...
2
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1answer
109 views

splitCsv map with text, join with another channel, nextflow

I have a csv file which describes number of chunks per chromosome, like; ...
2
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2answers
199 views

Use conditional in workflow in Nextflow dsl2

How should I do: ... if ($(params.aligner) == "bowtie") { align_bowtie2(get_fq_info.out.fq_info) } else { align_bwa(get_fq_info.out.fq_info) } ... ...
1
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2answers
149 views

Nextflow: Can I parameterize similar processes inside a for loop?

I have set of ~5 processes which perform very similar tasks such that their differences can be parameterized. Rather than putting 5 items through some channel (which seems complicated), or defining 5 ...
0
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0answers
191 views

parse csv/text file to create a channel with array in nextflow

[![example csv file][1]][1] First I want to start by parsing and doing some operation on a text/csv file. How could I read a csv/text file in nextflow? Suppose, I have above csv file with 3 columns. ...
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1answer
34 views

How to trigger next process on completion of previous process?

Simple question but I am stumped. (I am still learning Nextflow) I have a process which takes as input a channel of files and processes each file separately. There is a second process which needs to ...
1
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1answer
298 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: ...
1
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1answer
56 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: ...
1
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1answer
249 views

Nextflow: run sbatch (slurm job script) inside a process

I was trying to run a slurm job script inside nextflow process. Is it possible? For instance, I have a job script 'PRE_PHASING_QC.JOB' and outside nextflow it runs perfectly, I want to integrate it in ...
1
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1answer
86 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). Here is part my code block, any help?...
0
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1answer
141 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: ...
1
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1answer
110 views

Nextflow: ordering the execution of processes; outputs of process A are inputs of process B

I need to build a pipeline where 2nd process starts after completion of the 1st process and the 3rd after 2nd. As I understand nextflow's processes run parallel. But I need it to run in a order 1st>...
2
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1answer
82 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. My ...
1
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1answer
100 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 ...
1
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1answer
30 views

add task to nextflow and resume

in test.nf (dsl2) I have ... workflow{ a = Channel... processA(a) processB(processA.out.emitA) processC(processB.out.emitB) } ...
1
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2answers
195 views

How to merge back the processes by sample after splitting by chromosome in Nextflow?

I have a pipeline that has an input list of samples. I would like to split those samples by chromosomes, process each chromosome apart, and then merge them back by sample name. Here's an example: <...
1
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1answer
71 views

Master of Pores Installation Mac OS Mojave 10.14

I'm bit of a newbie with ONT analyses and am having some trouble with the Master Of Pores installation instructions (https://biocorecrg.github.io/master_of_pores/install.html). I've managed to install ...
0
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1answer
33 views

nextflow `fromPath` not passing all files with *

main.nf is #!/usr/bin/env nextflow params.input = '' tchan = Channel.fromFile(params.input) tchan.println() I have a.bam, b.bam and c.bam I run: ...
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0answers
99 views

Passing around complex metadata in Nextflow

I have a number of samples (from the 1000 genomes) that I want to analyse using Nextflow. However, I need to keep track of their metadata, fields like sample ID, analysis type etc. So I have a basic ...
3
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2answers
736 views

Run Nextflow with file dependencies inside a Docker container?

I’m trying to run a Nextflow workflow in a custom Docker container. Without Docker, the workflow succeeds. But running it inside the container leads to an error because a dependent file cannot be ...
3
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2answers
423 views

Autodetect max number of cores and pass as an argument in Nextflow

I am creating a pipeline in Nextflow. One step is creating a pangenome with Roary. Roary takes threads as an argument and if no number of threads is supplied as an argument it defaults to one. Is ...