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Matteo Schiavinato

2/2/23

Nextflow clean -f -but <mnemonic> behavior unclear

Hi, In my work I often use nextflow developing workflows as I go, figuring out the next step (ie the

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Nextflow clean -f -but <mnemonic> behavior unclear

Hi, In my work I often use nextflow developing workflows as I go, figuring out the next step (ie the

2/2/23

bio informatics, Matteo Schiavinato2

2/2/23

combine two channels by sample string

I think you're not assuming that the two channels have the same order, therefore you must combine

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combine two channels by sample string

I think you're not assuming that the two channels have the same order, therefore you must combine

2/2/23

ata...@gmail.com

12/9/22

cannot move files from work dir

Dear all, When I try to move some of my files from the workdir I get this error: Command error: mv:

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cannot move files from work dir

Dear all, When I try to move some of my files from the workdir I get this error: Command error: mv:

12/9/22

11/30/22

META: change Googlegroup email options to reflect deprecated status?

My understanding is that this Google Group has been deprecated in favor of using the Nextflow Slack.

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META: change Googlegroup email options to reflect deprecated status?

My understanding is that this Google Group has been deprecated in favor of using the Nextflow Slack.

11/30/22

Matteo Schiavinato, Alan Hoyle2

11/30/22

Using more than one node with Nextflow executor="local" (independent jobs)

Nextflow, by default, will only submit 100 jobs. https://www.nextflow.io/docs/latest/config.html#

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Using more than one node with Nextflow executor="local" (independent jobs)

Nextflow, by default, will only submit 100 jobs. https://www.nextflow.io/docs/latest/config.html#

11/30/22

11/3/22

Command exit status 127; /var/spool/slurmd/job16281783/slurm_script: line 1155: touch: command not found

Hi, I have a test nextflow script with multiple processes. One of the process is giving me the

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Command exit status 127; /var/spool/slurmd/job16281783/slurm_script: line 1155: touch: command not found

Hi, I have a test nextflow script with multiple processes. One of the process is giving me the

11/3/22

Gerardo Fabián, Anand2

10/22/22

Failed to pull singularity image

The recent recommendations have been to post your question to Nextflow Slack - https://www.nextflow.

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Failed to pull singularity image

The recent recommendations have been to post your question to Nextflow Slack - https://www.nextflow.

10/22/22

10/10/22

How to filter outputs from a directive

Hello all, I am performing QC on some genome assemblies, and want to only to include assemblies with

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How to filter outputs from a directive

Hello all, I am performing QC on some genome assemblies, and want to only to include assemblies with

10/10/22

9/27/22

Issues regarding python boto3 and nextflow syntax :(

Hi Everyone, my doubt is regarding Nextflow and boto3 python AWS services. I have prepared one boto3

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Issues regarding python boto3 and nextflow syntax :(

Hi Everyone, my doubt is regarding Nextflow and boto3 python AWS services. I have prepared one boto3

9/27/22

Adam Streck, Harshil Patel2

8/16/22

File Pairs as process input, DSL2

Hi Adam, Hope you are well! This group is no longer officially maintained in favour of using the

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File Pairs as process input, DSL2

Hi Adam, Hope you are well! This group is no longer officially maintained in favour of using the

8/16/22

GIANMARIO FERRAMONTI CONFIMPRESA E CONFIMEA

8/4/22

LA DEPUTATA ASSASSINA #CRISTINAROSSELLO UNITA AL PEDOFILO KILLER #FEDELECONFALONIERI FEDELE CONFALONIERI DI #MEDIASET MEDIASET ALIAS MAFIASET, COMPLOTTA A MORTE, EROI ANTI MAFIA E NAZISMO DI #SILVIOBERLUSCONI, SILVIO BERLUSCONI, #BERLUSCONI..........

LA DEPUTATA ASSASSINA #CRISTINAROSSELLO UNITA AL PEDOFILO KILLER #FEDELECONFALONIERI FEDELE

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LA DEPUTATA ASSASSINA #CRISTINAROSSELLO UNITA AL PEDOFILO KILLER #FEDELECONFALONIERI FEDELE CONFALONIERI DI #MEDIASET MEDIASET ALIAS MAFIASET, COMPLOTTA A MORTE, EROI ANTI MAFIA E NAZISMO DI #SILVIOBERLUSCONI, SILVIO BERLUSCONI, #BERLUSCONI..........

LA DEPUTATA ASSASSINA #CRISTINAROSSELLO UNITA AL PEDOFILO KILLER #FEDELECONFALONIERI FEDELE

8/4/22

7/15/22

Redirect output

Hi All Normally nextflow writes its output to $PWD/work. I would instead like to direct it to a

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Redirect output

Hi All Normally nextflow writes its output to $PWD/work. I would instead like to direct it to a

7/15/22

7/14/22

/bin/bash: .command.run: No such file or directory. When running Nextflow from inside a POD.

Sorry now, I observed that whenI enter into the work dir I can find the files: bash-4.4# cd /usr/src/

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/bin/bash: .command.run: No such file or directory. When running Nextflow from inside a POD.

Sorry now, I observed that whenI enter into the work dir I can find the files: bash-4.4# cd /usr/src/

7/14/22

Eldad Kdoshim, … drhp...@gmail.com5

6/29/22

Harshil, Thanks for the replay We don't need the sorting on the process, I want the resume to

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Harshil, Thanks for the replay We don't need the sorting on the process, I want the resume to

6/29/22

6/23/22

running nextflow on eks

Hi all, i'm trying to run nextflow from k8s node on Amazon Elastic Kubernetes service but I'm

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running nextflow on eks

Hi all, i'm trying to run nextflow from k8s node on Amazon Elastic Kubernetes service but I'm

6/23/22

Lauren Kleine, … Xin Gong10

6/16/22

Permission errors with docker and nextflow?

our sysadmin said id -g gives me primary group id. hard coding, docker.runOptions = ' -u <user

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Permission errors with docker and nextflow?

our sysadmin said id -g gives me primary group id. hard coding, docker.runOptions = ' -u <user

6/16/22

Philipp Diercks, Paolo Di Tommaso3

6/13/22

NFDI4Ing Scientific Workflow Requirements

Hi Paolo! thank you for your message. I am looking forward to that PR :) We encountered the same

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NFDI4Ing Scientific Workflow Requirements

Hi Paolo! thank you for your message. I am looking forward to that PR :) We encountered the same

6/13/22

6/10/22

nextflow kuberun is running into errors

Hi All, I've been trying to run nextflow on a kubernetes cluster which has a File storage mounted

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nextflow kuberun is running into errors

Hi All, I've been trying to run nextflow on a kubernetes cluster which has a File storage mounted

6/10/22

Elisabeth Ortega, Combiz2

6/8/22

Send folders from one process to the rest of the processes in a pipeline

Hi Elisabeth, I'd create a channel to read in the myFolder.tar.gz file (or *.tar.gz files). After

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Send folders from one process to the rest of the processes in a pipeline

Hi Elisabeth, I'd create a channel to read in the myFolder.tar.gz file (or *.tar.gz files). After

6/8/22

Elisabeth Ortega, Paolo Di Tommaso2

5/27/22

NextFlow and Apptainer

Nextflow does not have a built-in support for Apptainer. I'm wondering if Apptainer command line

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NextFlow and Apptainer

Nextflow does not have a built-in support for Apptainer. I'm wondering if Apptainer command line

5/27/22

Stephan Schmeing, … Kemin Zhou11

5/21/22

Running only part of a nextflow pipeline

I am also having similar needs. My pipeline is very long. Sometimes, we need to reprocess data for

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Running only part of a nextflow pipeline

I am also having similar needs. My pipeline is very long. Sometimes, we need to reprocess data for

5/21/22

5/19/22

why my process only open once

dear all: my code is grouplist2.splitCsv(header:false,sep:'\t').groupTuple().set{groups}

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why my process only open once

dear all: my code is grouplist2.splitCsv(header:false,sep:'\t').groupTuple().set{groups}

5/19/22

5/16/22

Slurm Executor not finding .command.run

Hi, I have a Nextflow script and a config here: https://gist.github.com/SabrinaJaye/

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Slurm Executor not finding .command.run

Hi, I have a Nextflow script and a config here: https://gist.github.com/SabrinaJaye/

5/16/22

5/3/22

memory specification with slurm AWS

Hello to all, I've been working for a few days on an HPC infrastructure on AWS with slurm. I

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memory specification with slurm AWS

Hello to all, I've been working for a few days on an HPC infrastructure on AWS with slurm. I

5/3/22

Doovesh Yash, Paolo Di Tommaso2

5/2/22

Integration of variants annotation tools

Hello, This project should help https://www.ensembl.info/2022/04/29/cool-stuff-ensembl-vep-can-do-run

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Integration of variants annotation tools

Hello, This project should help https://www.ensembl.info/2022/04/29/cool-stuff-ensembl-vep-can-do-run

5/2/22

EMILIENE BERINYUY

5/1/22

Nextflow error when running pipeline

Hi, I tried running a test dataset with a pipeline link (nextflow run bahlolab/PLASTER -profile

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Nextflow error when running pipeline

Hi, I tried running a test dataset with a pipeline link (nextflow run bahlolab/PLASTER -profile

5/1/22

5/1/22

Real time data analysis

Hi Guys, I want to watch files appear in a specified directory (eg /data/*.fq.gz) using a channel and

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Real time data analysis

Hi Guys, I want to watch files appear in a specified directory (eg /data/*.fq.gz) using a channel and

5/1/22

4/21/22

wrong variables assignment when calling groovy function under "script:"

Hey, I've noticed strange behaviour: Inside my NF script I've created a function, that just

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wrong variables assignment when calling groovy function under "script:"

Hey, I've noticed strange behaviour: Inside my NF script I've created a function, that just

4/21/22

Damian Loska, drhp...@gmail.com4

4/20/22

a process with conditional channel

Ah, so in that case you could try to always stage the intervals files for both types of prep. Might

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a process with conditional channel

Ah, so in that case you could try to always stage the intervals files for both types of prep. Might

4/20/22

Kemin Zhou, … drhp...@gmail.com3

4/20/22

what is exit status - negative sign

Hi Kemin, status: COMPLETED; exit: -; error: -; workDir: /data/work/7d/7c4c4872b319e4c1b6c6fbd8aa28d5

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what is exit status - negative sign

Hi Kemin, status: COMPLETED; exit: -; error: -; workDir: /data/work/7d/7c4c4872b319e4c1b6c6fbd8aa28d5

4/20/22

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