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3 votes
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Does PGS Catalog limit the number of queries to their FTP server?

I am calculating a polygenic risk score (PGS) from the PGS Catalog using the following command: ...
Cristian Riccio's user avatar
2 votes
0 answers
56 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 ...
Setshaba's user avatar
2 votes
0 answers
123 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 ...
Death Metal's user avatar
2 votes
0 answers
99 views

Problem with nextflow -resume and path.fromSRA

I have a problem with nextflow -resume Here is my script : ...
eva fonta's user avatar
1 vote
1 answer
183 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 ...
eva fonta's user avatar
1 vote
0 answers
223 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 ...
Migwell's user avatar
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0 answers
27 views

Why is my nextflow script executed sequentially?

I have the following Nextflow script: ...
MauriRamone's user avatar
0 votes
0 answers
607 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. ...
zillur rahman's user avatar