Questions tagged [nextflow]

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3 votes
1 answer
61 views

Nextflow: Properly chaining process outputs

I have written a pipeline that is composed of three processes. I seem to be misunderstanding how Nextflow passes the outputs from one process to the next or creates a queue of files. I am using a ...
2 votes
0 answers
44 views

Racon: empty overlap set!

Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then ...
1 vote
1 answer
157 views

Remove files after process is terminated

In my pipeline nextflow, I create a channel with channel.fromSRA and the channel contains lots of heavy files.fastq.gz. Then I have a first process to unzip files and transform them in files.fasta and ...
1 vote
1 answer
226 views

Export multiple variables from shell script into a Nextflow output channel

Within a Nextflow workflow, some process runs a shell script that creates multiple variables, e.g. ...
3 votes
1 answer
96 views

Error output in nextflow pipeline using fasterq-dump

I have one file with multiple SRA accession called Dataframe_with_accession.txt, for this example I just put one SRA in that file called :...
2 votes
1 answer
90 views

nextflow: merge lane files from samples forward and reverse read

I'd like to merge files from different lanes for forward and reverse reads. For e.g., if a sample A has three lanes in forward, and three reverse, ultimately one reverse and one forward is to be ...
1 vote
1 answer
78 views

nextflow: unable to find index

I've a pipeline with many processes. One of the steps is to run lancet tool. Lancet tool runs per chromosome (1-22, x,y). The input in the lancet step is output from the applybqsr (gatk). There are ...
1 vote
1 answer
152 views

Nextflow - Missing value declared as output parameter - output variable defined in script

I've normal-tumor human FASTQ file(s). Currently, I work with only one sample (both normal and tumor fastq R1 and R2), only. I have alignment gatk mark duplicates, setupnmdtags, applybqsr, recalibrate ...
4 votes
1 answer
118 views

nextflow: tumor normal sample - how to make code organic

I'm developing pipeline in nextflow it uses tools: fastp, bwa mem index, bwamem, gatk mark duplicates, gatk setupnmd, gatk applybqsr, gatk recalibrate. I do this using FASTQ.gz of normal and tumor DNA ...
2 votes
2 answers
784 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: <...
4 votes
1 answer
331 views

Nextflow - Process has already been used

I am trying to write a nextflow script below: ...
2 votes
0 answers
114 views

Nextflow: pass reads variable to process in another script

This question has been asked and answered on Stack Overflow I'm new to nextflow, channel, process. Kindly bear with me. I'd like to create a pipeline, pass paired reads from one to another process. I ...
4 votes
2 answers
204 views

Why does this nextflow script finish after running one sample?

I have 36 samples in total in the bam_files folder, with the name like this 20230306_CH_EP_C01.md.bam I expect the code to output all the 36 samples, one by one. But the run stopped after only running ...
3 votes
3 answers
301 views

Easier / lazy way to convert an existing bash pipeline to nextflow pipeline?

Not going to lie, my head hurts when I read the NextFlow documentation (No dig on the documentation, I think my head is losing its processing capacity lol). I had written a pipeline in Bash, ...
1 vote
1 answer
311 views

how to handle variable output from nextflow

I have this output which is going to do bwa next which is from join operator ...
2 votes
2 answers
484 views

How does one account for both single end and paired end reads as input in a Nextflow pipeline?

Suppose you have a pipeline that takes reads as input from the user and trims them. ...
3 votes
1 answer
561 views

Nextflow Error: failed to read header from "-"

I am trying to run my nextflow pipeline, and have gotten this error: samtools sort: failed to read header from "-" I'm not sure why this error is ...
3 votes
1 answer
256 views

Nextflow Pipeline: Unexpected Input "{"

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....
2 votes
1 answer
134 views

file order after nextflow groupTuple

Below is the code from nextflow site (https://www.nextflow.io/docs/edge/operator.html#grouptuple). For the output, the first is A B C, and the second is C, A. Is there a way to make the output like ...
3 votes
1 answer
275 views

Run nextflow pipeline multiple times depending on length of a list

This question was also asked on Stack Overflow I have a Nextflow pipeline that runs a BUSCO search on input data, returns the output and then creates a report based on the output. One of my parameters ...
2 votes
0 answers
96 views

Problem with nextflow -resume and path.fromSRA

I have a problem with nextflow -resume Here is my script : ...
2 votes
1 answer
280 views

Nextflow tuple from CSV cols

I am trying to create a channel with a CSV file and use it as tuple input. Yet the output I obtain does not contain the entire file but only the first element of the file (1st row). the csv ...
4 votes
1 answer
334 views

How to run a nextflow process for each file generated by another process separately - Input tuple does not match input set cardinality error

I have a process called FINDTAIL that generates different number of files depending on the input data. Its either 2 files or four files i.e. ...
3 votes
1 answer
405 views

How to handle output from a python script that gives different outputs depending upon the condition - Nextflow

I have created three Nextflow processes: One checks the strandedness of the fastq file and outputs it to a .txt file. Second one executes a python script with different commands depending upon the ...
2 votes
1 answer
235 views

Alignment process in Nextflow not picking up the index files from the index process

I'm using bowtie2 to build a small index. After building the index, I want to pass it to the bowtie2 alignment process. The issue is bowtie2-build outputs multiple index files with the .bt2 extension. ...
2 votes
1 answer
903 views

How to keep the basename of an input file and change its extension in Nextflow?

The following Nextflow scripts takes the $gtf as an input and outputs a .bed file. What I want is to keep just the basename of the gtf file and add the .bed extension to it. I tried declaring a ...
3 votes
1 answer
338 views

How to include only the trimmed fastq files into a nextflow channel and exclude any secondary log files created?

I have the following simple nextflow script, that takes fastq paired reads and runs them through the atria adapter trimming. ...
3 votes
1 answer
1k views

How to solve Nextflow error: "Trace file already exists"?

When trying to run epi2me-labs/wf-artic, I get the following error: ...
1 vote
1 answer
133 views

Only the first file Pair is processed from Channel.fromFilePairs()

This is my first nextflow pipeline and i am struggling with the .fromFilePairs concept of Nextflow. I want to process paired-end read files and align them against a reference genome. I use Hisat2 so ...
3 votes
1 answer
365 views

Using SED command in Nextflow script

I was wondering if someone can help me figure out this error message. I’m at the end of my Nextflow pipeline and I want to change the header in a FASTA file and it works when I use this command: ...
1 vote
1 answer
293 views

Nextflow with Minimap2 not working

I'm trying to create a Nextflow script that maps assemblies to reference gene sequences. This is what I have so far: ...
1 vote
1 answer
2k 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 ...
2 votes
1 answer
225 views

recover files after groupTuple

I have a process that emits BAM files with a key containing the sample name: ...
3 votes
1 answer
622 views

Nextflow scheduler job doesn't end upon successful workflow completion

Bug fixed This issue appears to have been fixed in latest Nextflow: https://github.com/nextflow-io/nextflow/issues/2693 I've been using ...
2 votes
1 answer
590 views

How can I call one file from a channel that's composed of several files in Nextflow?

In Nextflow I have a process that creates a channel that holds several files in a tuple. I'm trying to call only one of those files as input for a subsequent process. So basically if I run ...
2 votes
1 answer
528 views

Nextflow: cannot get file pairs from Channel.fromFilePairs

I'm remarkably still struggling with some basic Nextflow concepts. I'm simply trying to collect all pairs of .cram and ...
2 votes
1 answer
558 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....
4 votes
1 answer
551 views

BWA mem | samtools view: Intermittent parsing error

Update The issue was that bwa was running out of memory and failing, but that error wasn't floating to the top (see @Steve's answer, below). I was getting an error ...
6 votes
1 answer
1k views

Nextflow: dynamically setting resource directives for a process

I'm trying to test variations of CPU and memory for a specific process (samtools sort) to measure computational efficiency (measured only by time). To do this, I'd ...
5 votes
2 answers
2k views

Nextflow (DSL v2): how to best synchronize multiple outputs from a single process

I have a workflow that needs to: Generate .fastq files from .bams (while preserving the @RG ...
2 votes
1 answer
2k 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 ...
2 votes
2 answers
1k views

Nextflow: how to create many-to-many tuple for process

Using Nextflow, I need to submit x * y jobs where x is the number of input ...
2 votes
1 answer
701 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 ...
2 votes
1 answer
529 views

How fo force nextflow to repeat a process until all values in a particular channels are used up BUT a single value from another channel is needed

I am trying to find a hack for getting a process to run until all emissions in a channel are used up. The problem is that the process also takes as input a second channel that only has a single ...
4 votes
2 answers
649 views

use same output in two processes in nextflow dsl2

This is my workflow: ...
0 votes
1 answer
424 views

Nextflow HISAT2 command exit status 255 with prebuild index

I have a problem with my nextflow pipeline. My workflow looks like this: Uncompress the hisat2 genotpye index grch38_genome.tar.gz from https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz ...
0 votes
1 answer
774 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 vote
2 answers
585 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 <...
3 votes
1 answer
761 views

splitCsv map with text, join with another channel, nextflow

I have a csv file which describes number of chunks per chromosome, like; ...
1 vote
1 answer
108 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 ...