# \#workflow-options **URL:** https://help.galaxyproject.org/tag/workflow-options/294.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Jobs Stuck processing with a workflow: Using the job cache to rerun workflows with canceled outputs](https://help.galaxyproject.org/t/jobs-stuck-processing-with-a-workflow-using-the-job-cache-to-rerun-workflows-with-canceled-outputs/17659)
**Author:** [@M\_M](https://help.galaxyproject.org/u/M_M)\ **Replies:** 3\ **Last updated:** [April 21, 2026, 7:20pm UTC](https://help.galaxyproject.org/t/jobs-stuck-processing-with-a-workflow-using-the-job-cache-to-rerun-workflows-with-canceled-outputs/17659 "2026-04-21T19:20:14Z")
Hi, I’ve started a workflow with 42 samples. They were all scheduled for RNA Star, 5 hours later 39 samples were successfully completed. However, now 19 hours after the samples went into Star 2 are still processing. Is … --- ## [How to export History to file while keeping original sample names](https://help.galaxyproject.org/t/how-to-export-history-to-file-while-keeping-original-sample-names/17286)
**Author:** [@Onnodg](https://help.galaxyproject.org/u/Onnodg)\ **Replies:** 1\ **Last updated:** [January 20, 2026, 6:15pm UTC](https://help.galaxyproject.org/t/how-to-export-history-to-file-while-keeping-original-sample-names/17286 "2026-01-20T18:15:49Z")
Hello, I want to export a History, but when i download the whole history as a .rocrate map, my output files look like this: However, this way i cant group my results into the specific sites they belong to. Is there … --- ## [Rerunning only failed jobs in a workflow: Replace and Resume functions](https://help.galaxyproject.org/t/rerunning-only-failed-jobs-in-a-workflow-replace-and-resume-functions/16387)
**Author:** [@Koen\_Nijbroek](https://help.galaxyproject.org/u/Koen_Nijbroek)\ **Replies:** 4\ **Last updated:** [October 16, 2025, 10:00am UTC](https://help.galaxyproject.org/t/rerunning-only-failed-jobs-in-a-workflow-replace-and-resume-functions/16387 "2025-10-16T10:00:01Z")
Hello everyone! I’m running some massive workflows on a private Galaxy instance, with up to thousands of individual jobs. Occasionally it might happen that jobs crash - this is now I fear due to very short lasting lost … --- ## [Library dataset as input of a workflow](https://help.galaxyproject.org/t/library-dataset-as-input-of-a-workflow/16389)
**Author:** [@breakthewall](https://help.galaxyproject.org/u/breakthewall)\ **Replies:** 3\ **Last updated:** [October 15, 2025, 5:55pm UTC](https://help.galaxyproject.org/t/library-dataset-as-input-of-a-workflow/16389 "2025-10-15T17:55:14Z")
Hi, is it possible to set files from libraries as input dataset of a workflow, I mean in the workflow editor, as fixed parameter? Thanks --- ## [Workflows: job queues and managing partial failures with Resume and Replace!](https://help.galaxyproject.org/t/workflows-job-queues-and-managing-partial-failures-with-resume-and-replace/16371)
**Author:** [@bgood07](https://help.galaxyproject.org/u/bgood07)\ **Replies:** 3\ **Last updated:** [October 14, 2025, 6:45pm UTC](https://help.galaxyproject.org/t/workflows-job-queues-and-managing-partial-failures-with-resume-and-replace/16371 "2025-10-14T18:45:42Z")
Hello, I am using kraken2 on the galaxy Europe server to assign taxonomic labels to shotgun sequencing reads. I created a paired end list of the samples and then used trimmomatic to trim reads. I then used the trimmomati… --- ## [Optional steps in workflow can't be connected to one another](https://help.galaxyproject.org/t/optional-steps-in-workflow-cant-be-connected-to-one-another/16120)
**Author:** [@taulagnon](https://help.galaxyproject.org/u/taulagnon)\ **Replies:** 2\ **Last updated:** [August 7, 2025, 9:47am UTC](https://help.galaxyproject.org/t/optional-steps-in-workflow-cant-be-connected-to-one-another/16120 "2025-08-07T09:47:15Z")
Hello ! I’m currently building a workflow in which I’d like to have an optional Kraken2 / Krona step, which the user could toggle on or off. I’ve been trying to use a boolean input in order to implement that, but for s… --- ## [VGP- unable to select or add hind3 restriction enzyme to Hi-C scaffolding workflow](https://help.galaxyproject.org/t/vgp-unable-to-select-or-add-hind3-restriction-enzyme-to-hi-c-scaffolding-workflow/13406)
**Author:** [@HT87](https://help.galaxyproject.org/u/HT87)\ **Replies:** 1\ **Last updated:** [September 10, 2024, 7:29pm UTC](https://help.galaxyproject.org/t/vgp-unable-to-select-or-add-hind3-restriction-enzyme-to-hi-c-scaffolding-workflow/13406 "2024-09-10T19:29:39Z")
Hello, I noticed that VGP Hi-C scaffolding workflow does provide few selections for restriction enzyme input and does not allow a custom input. I used HindIII in my Hi-C library which have recognition site on AAGCTT. H… --- ## [CutAdapt adapter file in Galaxy workflow](https://help.galaxyproject.org/t/cutadapt-adapter-file-in-galaxy-workflow/10536)
**Author:** [@Priyanka\_Bhandary](https://help.galaxyproject.org/u/Priyanka_Bhandary)\ **Replies:** 2\ **Last updated:** [August 1, 2023, 10:39pm UTC](https://help.galaxyproject.org/t/cutadapt-adapter-file-in-galaxy-workflow/10536 "2023-08-01T22:39:36Z")
Hello, I am the admin for the Galaxy instance that we use at our institution, which is connected to a High-performance cluster as well. I have developed an RNA-Seq Primary analysis workflow and have incorporated “CutAda… --- ## [Nanoplot - Configure output - Rename dataset](https://help.galaxyproject.org/t/nanoplot-configure-output-rename-dataset/9816)
**Author:** [@jessemartin](https://help.galaxyproject.org/u/jessemartin)\ **Replies:** 3\ **Last updated:** [July 24, 2023, 10:20am UTC](https://help.galaxyproject.org/t/nanoplot-configure-output-rename-dataset/9816 "2023-07-24T10:20:20Z")
Hi There, Can anybody help me with renaming the output dataset in Nanoplot - I have managed to successfully change the output name for all the other tools in my workflow but i cant seem to get it to work with Nanoplot. … --- ## [How to resume a workflow after a step fails](https://help.galaxyproject.org/t/how-to-resume-a-workflow-after-a-step-fails/4643)
**Author:** [@yingfeng-iu](https://help.galaxyproject.org/u/yingfeng-iu)\ **Replies:** 3\ **Last updated:** [July 6, 2022, 6:04pm UTC](https://help.galaxyproject.org/t/how-to-resume-a-workflow-after-a-step-fails/4643 "2022-07-06T18:04:26Z")
Hello! If a workflow fails on a certain step, after fixing whatever issue causing it, what’s the best way to resume that step and let the workflow continue? I don’t mean to rerun that step (like using the rerun button on… --- ## [Workflow execution stalled](https://help.galaxyproject.org/t/workflow-execution-stalled/5357)
**Author:** [@THYeh](https://help.galaxyproject.org/u/THYeh)\ **Replies:** 4\ **Last updated:** [February 11, 2021, 5:41pm UTC](https://help.galaxyproject.org/t/workflow-execution-stalled/5357 "2021-02-11T17:41:49Z")
Having the same problem posted in this thread (Cannot run my workflow - #2 by BenSamy2020). Individual analysis works fine, but when running workflow, it started successfully with the green check box, but then nothing ha… --- ## [Input file deleted mid-workflow](https://help.galaxyproject.org/t/input-file-deleted-mid-workflow/2609)
**Author:** [@ahbedard](https://help.galaxyproject.org/u/ahbedard)\ **Replies:** 1\ **Last updated:** [December 6, 2019, 6:18pm UTC](https://help.galaxyproject.org/t/input-file-deleted-mid-workflow/2609 "2019-12-06T18:18:33Z")
I have been running a few different workflows successfully as of late (read alignment/quant to transcriptome w/ Salmon). However, recently my fasta.gz transcriptome input file seems to be randomly deleted in the middle o…