# Ask for help **URL:** https://community.seqera.io/c/help/37.md [Latest](https://community.seqera.io/latest.md) · [Categories](https://community.seqera.io/categories.md) · [Tags](https://community.seqera.io/tags.md) --- ## [About the Ask for help category](https://community.seqera.io/t/about-the-ask-for-help-category/124)
**Author:** [@ewels](https://community.seqera.io/u/ewels)\ **Replies:** 0
There are no stupid questions! Not sure where to start, but something’s not working? If in doubt, create a new topic here to ask for help from the communuity. If someone solves your issue, please remember to mark that … --- ## [Container Entrypoint](https://community.seqera.io/t/container-entrypoint/2774)
**Author:** [@Sam\_H](https://community.seqera.io/u/Sam_H)\ **Replies:** 0\ **Last updated:** [October 6, 2026, 11:10am UTC](https://community.seqera.io/t/container-entrypoint/2774 "2026-10-06T11:10:37Z")
Hi everybody, I’m trying to build a Nextflow workflow using podman containers. The docs state: Bash must be available at /bin/bash and must be the container entrypoint. However, it seems the opposite is true: A cont… --- ## [Modify an input parameter based on another input parameter](https://community.seqera.io/t/modify-an-input-parameter-based-on-another-input-parameter/2770)
**Author:** [@wanamalauasha](https://community.seqera.io/u/wanamalauasha)\ **Replies:** 1\ **Last updated:** [October 1, 2026, 1:26pm UTC](https://community.seqera.io/t/modify-an-input-parameter-based-on-another-input-parameter/2770 "2026-10-01T13:26:33Z")
Hi! Is it possible to modify an input parameter based on another input parameter? Which is the best way to do it, through the configuration file or directly within the process? In my config file: params { initial\_… --- ## [Nxf\_unstage\_output(): ls fails when dealing with very large number of files](https://community.seqera.io/t/nxf-unstage-output-ls-fails-when-dealing-with-very-large-number-of-files/2761)
**Author:** [@TheoG](https://community.seqera.io/u/TheoG)\ **Replies:** 2\ **Last updated:** [September 15, 2026, 12:01pm UTC](https://community.seqera.io/t/nxf-unstage-output-ls-fails-when-dealing-with-very-large-number-of-files/2761 "2026-09-15T12:01:01Z")
Hello, A bug I encountered when running my pipeline on a large dataset. The failing process is dockerized (hence the staging in/out) and exports a bunch of files through globing: output: path("${params.repref… --- ## [Question about the quiz](https://community.seqera.io/t/question-about-the-quiz/2764)
**Author:** [@Pegah\_Taklifi](https://community.seqera.io/u/Pegah_Taklifi)\ **Replies:** 2\ **Last updated:** [September 15, 2026, 2:40am UTC](https://community.seqera.io/t/question-about-the-quiz/2764 "2026-09-15T02:40:30Z")
I missed the beginning of today’s opening session and was wondering how I can participate in the quiz. Could you also let me know whether there are any assignments I should complete after each lesson on the training port… --- ## [Header contains h1 font size](https://community.seqera.io/t/header-contains-h1-font-size/2760)
**Author:** [@Hanjiewu](https://community.seqera.io/u/Hanjiewu)\ **Replies:** 3\ **Last updated:** [September 11, 2026, 8:07am UTC](https://community.seqera.io/t/header-contains-h1-font-size/2760 "2026-09-11T08:07:33Z")
When using a MultiQC custom content table, I noticed that column headers containing strings such as h1 and h2 are displayed with a different font size in the generated HTML report. For example, if the custom table conta… --- ## [Containers, tls certificates and Seqera plateform](https://community.seqera.io/t/containers-tls-certificates-and-seqera-plateform/2757)
**Author:** [@TheoG](https://community.seqera.io/u/TheoG)\ **Replies:** 4\ **Last updated:** [September 9, 2026, 3:08pm UTC](https://community.seqera.io/t/containers-tls-certificates-and-seqera-plateform/2757 "2026-09-09T15:08:16Z")
Hi there, I am testing a container created through Containers | Seqera with the ncbi-datasets-cli First container Simple container, only ncbi-datasets-cli=18.36.0 installed (conda-forge channel), image build details … --- ## [Channel enumerate](https://community.seqera.io/t/channel-enumerate/2754)
**Author:** [@TheoG](https://community.seqera.io/u/TheoG)\ **Replies:** 4\ **Last updated:** [September 8, 2026, 8:06am UTC](https://community.seqera.io/t/channel-enumerate/2754 "2026-09-08T08:06:10Z")
Hello, Maybe it is something available in the underlying Groovy language, but not something I could find through a quick web search. For my use case, I need to be able to “enumerate” a channel, ie simply get the index/… --- ## [Running Nextflow on AWS batch](https://community.seqera.io/t/running-nextflow-on-aws-batch/2750)
**Author:** [@tanasa](https://community.seqera.io/u/tanasa)\ **Replies:** 2\ **Last updated:** [September 3, 2026, 8:09pm UTC](https://community.seqera.io/t/running-nextflow-on-aws-batch/2750 "2026-09-03T20:09:39Z")
@GeraldineVdA @Geraldine Dear Nextflow community, We’re running Nextflow on AWS Batch (EC2, ECS AL2023, with an S3 work directory). The tool images don’t include the AWS CLI, so we use \`aws.batch.cliPath\` to mount a hos… --- ## [Seqera platform UI](https://community.seqera.io/t/seqera-platform-ui/2722)
**Author:** [@TheoG](https://community.seqera.io/u/TheoG)\ **Replies:** 1\ **Last updated:** [August 12, 2026, 11:23am UTC](https://community.seqera.io/t/seqera-platform-ui/2722 "2026-08-12T11:23:51Z")
Hello, A few suggestions/remarks about Seqera platform UI. Run \> Tasks \> Processes I find the progress bar and associated numbers quite confusing: In xx of yy , xx corresponds to the number of succeeded processes … --- ## [Control over processes and instances](https://community.seqera.io/t/control-over-processes-and-instances/2723)
**Author:** [@TheoG](https://community.seqera.io/u/TheoG)\ **Replies:** 1\ **Last updated:** [August 11, 2026, 11:09pm UTC](https://community.seqera.io/t/control-over-processes-and-instances/2723 "2026-08-11T23:09:18Z")
Hello, I am unsure whether this comes from Nextflow, Seqera platform, AWS, interactions between this components, or me setting bad configurations. I have the feeling that my workflows do not have the most efficient res… --- ## [Seqera\_workspace\_participant: role = "view" silently ignored during Create](https://community.seqera.io/t/seqera-workspace-participant-role-view-silently-ignored-during-create/2743)
**Author:** [@Piyumi\_Amarasinghe\_B](https://community.seqera.io/u/Piyumi_Amarasinghe_B)\ **Replies:** 2\ **Last updated:** [August 10, 2026, 1:41am UTC](https://community.seqera.io/t/seqera-workspace-participant-role-view-silently-ignored-during-create/2743 "2026-08-10T01:41:51Z")
Hi Team, I’m trying to add new participants to a workspace programmatically. I’m using the latest Seqera terraform provider (0.42.0). In my case, as our infrastructure is mainly managed using Pulumi, I generated the pul… --- ## [Installing the plugin from source](https://community.seqera.io/t/installing-the-plugin-from-source/2738)
**Author:** [@magletdinov](https://community.seqera.io/u/magletdinov)\ **Replies:** 0\ **Last updated:** [July 28, 2026, 10:59am UTC](https://community.seqera.io/t/installing-the-plugin-from-source/2738 "2026-07-28T10:59:25Z")
Hello everyone! I want to install the nf-weblog plugin on a server with network restrictions. The nextflow documentation says the correct way to do this is: Install a self-contained version of Nextflow in an environmen… --- ## [Scheduler pending reasons](https://community.seqera.io/t/scheduler-pending-reasons/2736)
**Author:** [@Cen\_T](https://community.seqera.io/u/Cen_T)\ **Replies:** 0\ **Last updated:** [July 27, 2026, 2:28pm UTC](https://community.seqera.io/t/scheduler-pending-reasons/2736 "2026-07-27T14:28:38Z")
Hi everyone, Currently, I’m using trace.txt to get jobs’ status. This works well once tasks start executing. However, I’ve noticed that when jobs are still pending in the scheduler (for example, Slurm jobs in PD state d… --- ## [How to properly add cellrangermulti vdj reference](https://community.seqera.io/t/how-to-properly-add-cellrangermulti-vdj-reference/2734)
**Author:** [@marcelcosta](https://community.seqera.io/u/marcelcosta)\ **Replies:** 1\ **Last updated:** [July 27, 2026, 8:54am UTC](https://community.seqera.io/t/how-to-properly-add-cellrangermulti-vdj-reference/2734 "2026-07-27T08:54:40Z")
Hi! I am trying to use scrnaseq pipeline for GEX+TCR analysis with cellranger multi pipeline. I am struggling with the VDJ reference parameters. This is my launcher command: NXF\_VER=25.10.4 nextflow run nf-core/scrnas… --- ## [How to handle in Nextflow docker mounting of symlinked files within a symlinked directory](https://community.seqera.io/t/how-to-handle-in-nextflow-docker-mounting-of-symlinked-files-within-a-symlinked-directory/2381)
**Author:** [@jfy133](https://community.seqera.io/u/jfy133)\ **Replies:** 5\ **Last updated:** [July 27, 2026, 8:23am UTC](https://community.seqera.io/t/how-to-handle-in-nextflow-docker-mounting-of-symlinked-files-within-a-symlinked-directory/2381 "2026-07-27T08:23:04Z")
I’m struggling with an issue with nf-core modules I have made for building Kraken2. For context, Kraken2 uses a directory as a database. To build the database, you have to execute two separate commands. In the first ste… --- ## [Using local reference instead of connecting to iGenome](https://community.seqera.io/t/using-local-reference-instead-of-connecting-to-igenome/2724)
**Author:** [@marcelcosta](https://community.seqera.io/u/marcelcosta)\ **Replies:** 2\ **Last updated:** [July 22, 2026, 1:07pm UTC](https://community.seqera.io/t/using-local-reference-instead-of-connecting-to-igenome/2724 "2026-07-22T13:07:32Z")
Hi! I am trying to run “scRNAseq” nf-core pipeline with that command: NXF\_VER=25.10.4 nextflow run nf-core/scrnaseq \\ -profile test \\ --aligner cellranger \\ --fasta ~/Shared-MarcelCosta/apps/cellranger-10.0… --- ## [Seqera x AWS problem?](https://community.seqera.io/t/seqera-x-aws-problem/2721)
**Author:** [@TheoG](https://community.seqera.io/u/TheoG)\ **Replies:** 3\ **Last updated:** [July 14, 2026, 9:56am UTC](https://community.seqera.io/t/seqera-x-aws-problem/2721 "2026-07-14T09:56:22Z")
Hello, I am encountering problems running pipelines through Seqera platform. My runs are stuck as “submitted”, when I check through AWS console, there is no job in any AWS Batch queue. I just tried running an “hello w… --- ## [Priority control in custom nextflow pipeline](https://community.seqera.io/t/priority-control-in-custom-nextflow-pipeline/2717)
**Author:** [@Ankit\_Verma](https://community.seqera.io/u/Ankit_Verma)\ **Replies:** 3\ **Last updated:** [July 13, 2026, 5:13pm UTC](https://community.seqera.io/t/priority-control-in-custom-nextflow-pipeline/2717 "2026-07-13T17:13:19Z")
Hi team, I have a question regarding changing the priority of samples while they are already running through the analysis pipeline. Our team has designed a custom Nextflow pipeline where each sample is assigned an init… --- ## [Different output mode for different processes](https://community.seqera.io/t/different-output-mode-for-different-processes/2719)
**Author:** [@fragilefort](https://community.seqera.io/u/fragilefort)\ **Replies:** 2\ **Last updated:** [July 7, 2026, 2:16pm UTC](https://community.seqera.io/t/different-output-mode-for-different-processes/2719 "2026-07-07T14:16:47Z")
Hi, so I am publishing these different outputs in my main wf: output { merged\_reads { path { meta, \_reads -\> "merged\_reads/${meta.donor}" } } qc\_html { path { meta, \_html -\> "fastqc/html/${meta.donor}" } mode 'cop… --- ## ['which' is missing in recent seqera containers](https://community.seqera.io/t/which-is-missing-in-recent-seqera-containers/2718)
**Author:** [@Nico\_Trummer](https://community.seqera.io/u/Nico_Trummer)\ **Replies:** 2\ **Last updated:** [July 6, 2026, 1:01pm UTC](https://community.seqera.io/t/which-is-missing-in-recent-seqera-containers/2718 "2026-07-06T13:01:48Z")
A simple r-base container currently does not work: This is because which is missing from the container. When comparing current build URLs with older ones, I saw that the base image changed. So I compared the base ima… --- ## [Nextflow 26.04 and parser v2 : About multiple input and output processs](https://community.seqera.io/t/nextflow-26-04-and-parser-v2-about-multiple-input-and-output-processs/2714)
**Author:** [@mg-btiger](https://community.seqera.io/u/mg-btiger)\ **Replies:** 4\ **Last updated:** [June 25, 2026, 11:54am UTC](https://community.seqera.io/t/nextflow-26-04-and-parser-v2-about-multiple-input-and-output-processs/2714 "2026-06-25T11:54:47Z")
Hello. I encounter a problem with running my pipeline concerning the assembly and annotation of bacterial genomes. I am new using Nextflow since v25.10 and now i updated it to the newer version 26.04. My pipeline ran wel… --- ## [Setting worker pool](https://community.seqera.io/t/setting-worker-pool/2665)
**Author:** [@dommas](https://community.seqera.io/u/dommas)\ **Replies:** 4\ **Last updated:** [June 19, 2026, 1:50pm UTC](https://community.seqera.io/t/setting-worker-pool/2665 "2026-06-19T13:50:42Z")
Hi, I noticed an undocumented workerPool option in the Compute Environment API for Azure Batch. I recently updated our Seqera integration to use separate node pools for head and compute workloads. Since I couldn’t find … --- ## [Error connecting to Seqera MCP API in VSCode (unknown client during browser authentication)](https://community.seqera.io/t/error-connecting-to-seqera-mcp-api-in-vscode-unknown-client-during-browser-authentication/2609)
**Author:** [@tnmquann](https://community.seqera.io/u/tnmquann)\ **Replies:** 1\ **Last updated:** [June 16, 2026, 8:07pm UTC](https://community.seqera.io/t/error-connecting-to-seqera-mcp-api-in-vscode-unknown-client-during-browser-authentication/2609 "2026-06-16T20:07:07Z")
Hi, I encountered an error when connecting to the Seqera MCP API. Environment Operating System: Windows 11 Application: VSCode v1.111.0 Issue When Seqera MCP opens the browser for authentication, the login process … --- ## [Force rebuild of container](https://community.seqera.io/t/force-rebuild-of-container/2348)
**Author:** [@Schmytzi](https://community.seqera.io/u/Schmytzi)\ **Replies:** 2\ **Last updated:** [June 9, 2026, 3:06pm UTC](https://community.seqera.io/t/force-rebuild-of-container/2348 "2026-06-09T15:06:34Z")
Is there a way to force Seqera Containers to rebuild a container? I am trying to retrieve one for ont-modkit version 0.5.0. The Singularity container works fine but modkit identifies itself as version 0.4.5 instead of 0.… --- ## [Different containers for different processes (running nextflow in offline mode)](https://community.seqera.io/t/different-containers-for-different-processes-running-nextflow-in-offline-mode/2705)
**Author:** [@Maulik\_Upadhyay](https://community.seqera.io/u/Maulik_Upadhyay)\ **Replies:** 3\ **Last updated:** [June 9, 2026, 2:05pm UTC](https://community.seqera.io/t/different-containers-for-different-processes-running-nextflow-in-offline-mode/2705 "2026-06-09T14:05:32Z")
I am trying to run a Nextflow workflow offline using two different Apptainer containers that are already downloaded and stored in my home directory. The workflow is intended to use: One container exclusively for the M… --- ## [Seqera Platform ending with .command.run line 178 bash error on all scripts staging files](https://community.seqera.io/t/seqera-platform-ending-with-command-run-line-178-bash-error-on-all-scripts-staging-files/2703)
**Author:** [@Marco\_Blanchette](https://community.seqera.io/u/Marco_Blanchette)\ **Replies:** 2\ **Last updated:** [June 4, 2026, 4:17pm UTC](https://community.seqera.io/t/seqera-platform-ending-with-command-run-line-178-bash-error-on-all-scripts-staging-files/2703 "2026-06-04T16:17:18Z")
Hi, I have been using Seqera platform for many years now and for some reason, a few weeks ago, all my previous pipeline that use to complete successfully now all errors with the same bash error from the .command.run scr… --- ## [Syntax parser v2: run parameter not automatically set from workflow launchpad parameter?](https://community.seqera.io/t/syntax-parser-v2-run-parameter-not-automatically-set-from-workflow-launchpad-parameter/2695)
**Author:** [@TheoG](https://community.seqera.io/u/TheoG)\ **Replies:** 4\ **Last updated:** [June 4, 2026, 1:50pm UTC](https://community.seqera.io/t/syntax-parser-v2-run-parameter-not-automatically-set-from-workflow-launchpad-parameter/2695 "2026-06-04T13:50:25Z")
Hello, I have a workflow that I added to the launchpad and parameterised to use Syntax Parser v2: When launching a run from this workflow, the option is not automatically set: I am not sure this is the expected … --- ## [Versioning Question for the nf-core/pacvar Release](https://community.seqera.io/t/versioning-question-for-the-nf-core-pacvar-release/2690)
**Author:** [@chaochaowong](https://community.seqera.io/u/chaochaowong)\ **Replies:** 2\ **Last updated:** [June 4, 2026, 10:06am UTC](https://community.seqera.io/t/versioning-question-for-the-nf-core-pacvar-release/2690 "2026-06-04T10:06:34Z")
The current release version of pacvar is 1.0.1 (first metro below). Since then, we have added six major modules to the pipeline (second metro belowO: hificnv (copy number variats), pbmerge (to merge fail bam), sawfish (s… --- ## [Problem with setting AWS Batch IAM credentials following new instructions](https://community.seqera.io/t/problem-with-setting-aws-batch-iam-credentials-following-new-instructions/2702)
**Author:** [@Marco\_Blanchette](https://community.seqera.io/u/Marco_Blanchette)\ **Replies:** 2\ **Last updated:** [June 4, 2026, 8:58am UTC](https://community.seqera.io/t/problem-with-setting-aws-batch-iam-credentials-following-new-instructions/2702 "2026-06-04T08:58:11Z")
Hi, I have been using Seqera platform for years, but I recently had a to create a new user for a new AWS account. I am following the new instructions found here AWS Batch | Seqera Docs First off, seems like there are tw… [Next page](https://community.seqera.io/c/help/37.md?page=1)