# Latest **URL:** https://cwl.discourse.group/latest.md?page=1 [Latest](https://cwl.discourse.group/latest.md) · [Categories](https://cwl.discourse.group/categories.md) **Page:** 2 --- ## [How to invoke GPU Docker usage](https://cwl.discourse.group/t/how-to-invoke-gpu-docker-usage/974)
**Author:** [@pennycuda](https://cwl.discourse.group/u/pennycuda)\ **Replies:** 1\ **Last updated:** [January 24, 2025, 8:13pm UTC](https://cwl.discourse.group/t/how-to-invoke-gpu-docker-usage/974 "2025-01-24T20:13:25Z")
Hello! I am a research programmer for HuBMAP Consortium. We currently have our own cwltool fork for CUDA usage in our workflows, but we would like to use the standard cwltool version if possible. Basically, I need cwltoo… --- ## [Validation does not catch missing inputs in conditional expression](https://cwl.discourse.group/t/validation-does-not-catch-missing-inputs-in-conditional-expression/971)
**Author:** [@lonbar](https://cwl.discourse.group/u/lonbar)\ **Replies:** 0\ **Last updated:** [January 22, 2025, 2:17pm UTC](https://cwl.discourse.group/t/validation-does-not-catch-missing-inputs-in-conditional-expression/971 "2025-01-22T14:17:28Z")
I recently noticed a mistake in one of my workflows. Whilst it was easily fixed, it made me wonder if cwltool’s validation correctly checks inputs in conditional expressions. Consider the following example: $ cat $PWD/… --- ## [Grouping outputs into separate directories](https://cwl.discourse.group/t/grouping-outputs-into-separate-directories/965)
**Author:** [@skgo](https://cwl.discourse.group/u/skgo)\ **Replies:** 0\ **Last updated:** [December 10, 2024, 7:44pm UTC](https://cwl.discourse.group/t/grouping-outputs-into-separate-directories/965 "2024-12-10T19:44:51Z")
Is there a straightforward way to group outputs from specific steps into different output directories? For example, say my workflow is something like trim → align → call variants → qc. I would like to group the results (… --- ## [Loading missing://](https://cwl.discourse.group/t/loading-missing/964)
**Author:** [@peterg1t](https://cwl.discourse.group/u/peterg1t)\ **Replies:** 2\ **Last updated:** [December 4, 2024, 8:42pm UTC](https://cwl.discourse.group/t/loading-missing/964 "2024-12-04T20:42:45Z")
I was revisiting a pipeline and this exception showed up. Got exception 'No available job store implementation can import the URL 'missing:'. Ensure Toil has been installed with the appropriate extras.' while copying 'm… --- ## [Use inline javascript when specifying input string](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963)
**Author:** [@skgo](https://cwl.discourse.group/u/skgo)\ **Replies:** 5\ **Last updated:** [December 3, 2024, 5:06pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963 "2024-12-03T17:06:04Z")
Is it possible to use inline javascript in order to construct an input string in a workflow? Below is an example of my workflow: cwlVersion: v1.2 class: Workflow requirements: InlineJavascriptRequirement: {} inputs:… --- ## ["Singularity exec" vs "docker run"](https://cwl.discourse.group/t/singularity-exec-vs-docker-run/956)
**Author:** [@Samee](https://cwl.discourse.group/u/Samee)\ **Replies:** 6\ **Last updated:** [November 12, 2024, 3:38pm UTC](https://cwl.discourse.group/t/singularity-exec-vs-docker-run/956 "2024-11-12T15:38:48Z")
Hi there! New CWL/Toil user here. We have a workflow where we noticed that depending on whether singularity or docker container choice it uses exec vs run. I am trying to understand what was the rational behind this dif… --- ## [How to gather output files from subdirectories](https://cwl.discourse.group/t/how-to-gather-output-files-from-subdirectories/958)
**Author:** [@ndonyapour](https://cwl.discourse.group/u/ndonyapour)\ **Replies:** 1\ **Last updated:** [November 11, 2024, 9:11am UTC](https://cwl.discourse.group/t/how-to-gather-output-files-from-subdirectories/958 "2024-11-11T09:11:15Z")
Hello, I have a tool that downloads a database with image files saved in subdirectories within the output folder. I’m writing a CWL for this tool to gather the files from these subdirectories, but it fails because input… --- ## [How to run a bash command within a tool?](https://cwl.discourse.group/t/how-to-run-a-bash-command-within-a-tool/952)
**Author:** [@kvertacnik](https://cwl.discourse.group/u/kvertacnik)\ **Replies:** 3\ **Last updated:** [November 5, 2024, 11:12pm UTC](https://cwl.discourse.group/t/how-to-run-a-bash-command-within-a-tool/952 "2024-11-05T23:12:08Z")
I have a tool that utilizes a singularity container, however, I am on an HPC where the singularity module must be loaded prior to using a container. The command for this is “module load singularity”. I’m trying to load … --- ## [How to use arrays as input](https://cwl.discourse.group/t/how-to-use-arrays-as-input/954)
**Author:** [@kvertacnik](https://cwl.discourse.group/u/kvertacnik)\ **Replies:** 3\ **Last updated:** [November 5, 2024, 2:41pm UTC](https://cwl.discourse.group/t/how-to-use-arrays-as-input/954 "2024-11-05T14:41:59Z")
Apologies for the basic question. I have gff and genome file pairs that I would like to process together, however, the number of file pairs will vary. So I’m trying to input arrays of file pairs. The error I’m getting is… --- ## [Using a local Dockerfile based on renv.lock](https://cwl.discourse.group/t/using-a-local-dockerfile-based-on-renv-lock/941)
**Author:** [@Brilator](https://cwl.discourse.group/u/Brilator)\ **Replies:** 1\ **Last updated:** [November 5, 2024, 1:07pm UTC](https://cwl.discourse.group/t/using-a-local-dockerfile-based-on-renv-lock/941 "2024-11-05T13:07:33Z")
Hi everyone, in order to use and share an R script with CWL, I am trying to create and reference a Dockerfile based on the R package renv; mostly following the renv + docker instructions: (Using renv with Docker • renv … --- ## [Cwltool/provenance worfklow.cwl#main vs workflow.cwl](https://cwl.discourse.group/t/cwltool-provenance-worfklow-cwl-main-vs-workflow-cwl/948)
**Author:** [@FabriceBrito](https://cwl.discourse.group/u/FabriceBrito)\ **Replies:** 0\ **Last updated:** [September 2, 2024, 3:00pm UTC](https://cwl.discourse.group/t/cwltool-provenance-worfklow-cwl-main-vs-workflow-cwl/948 "2024-09-02T15:00:25Z")
I think I ran into a small issue in cwltool. cwltool --provenance /tmp/provenance workflow.cwl#main params.yml works fine, instead cwltool --provenance /tmp/provenance app-package.cwl params.yml throws an exception: E… --- ## [ExpressionTools loadContents how to load from array](https://cwl.discourse.group/t/expressiontools-loadcontents-how-to-load-from-array/947)
**Author:** [@CloXD](https://cwl.discourse.group/u/CloXD)\ **Replies:** 0\ **Last updated:** [August 29, 2024, 12:30pm UTC](https://cwl.discourse.group/t/expressiontools-loadcontents-how-to-load-from-array/947 "2024-08-29T12:30:56Z")
Hello! I’m trying to concatenate the content of some small files using the ExpressionTool, but it seems that the loadContents doesn’t work on arrays, despite in the doc it includes arrays of files. Here’s a small examp… --- ## [How to use the Docker installed libraries in a cwl workflow?](https://cwl.discourse.group/t/how-to-use-the-docker-installed-libraries-in-a-cwl-workflow/944)
**Author:** [@rupert\_may](https://cwl.discourse.group/u/rupert_may)\ **Replies:** 4\ **Last updated:** [August 19, 2024, 1:40pm UTC](https://cwl.discourse.group/t/how-to-use-the-docker-installed-libraries-in-a-cwl-workflow/944 "2024-08-19T13:40:15Z")
Hello, I am creating a cwl workflow, where I am writing the steps to run. The first step is regarding a Docker container, which is used to install some Python libraries. Then, I want the other cwl files to point to the … --- ## [Workflow fails when run without --cachedir](https://cwl.discourse.group/t/workflow-fails-when-run-without-cachedir/942)
**Author:** [@Brilator](https://cwl.discourse.group/u/Brilator)\ **Replies:** 2\ **Last updated:** [August 13, 2024, 11:39am UTC](https://cwl.discourse.group/t/workflow-fails-when-run-without-cachedir/942 "2024-08-13T11:39:32Z")
Hi, can someone help me understand allocating resources to workflows? I’m trying to run a rather simple workflow, scattered over an array of inputs (i.e. samples). Per sample the workflow creates ca. 10GB temporary dat… --- ## [Using a workflow input in a step\`s valueFrom](https://cwl.discourse.group/t/using-a-workflow-input-in-a-step-s-valuefrom/940)
**Author:** [@Brilator](https://cwl.discourse.group/u/Brilator)\ **Replies:** 2\ **Last updated:** [August 5, 2024, 6:35am UTC](https://cwl.discourse.group/t/using-a-workflow-input-in-a-step-s-valuefrom/940 "2024-08-05T06:35:49Z")
Hi CWL folks, I’m trying to use an input from a workflow’s inputs section as a variable in a valueFrom expression. The following works, but hardcodes to extract a substring of 11 characters from nameroot: cwlVersion: … --- ## [Graphical User Interface like Rabix Composer](https://cwl.discourse.group/t/graphical-user-interface-like-rabix-composer/934)
**Author:** [@Echelon\_Bioanalytics](https://cwl.discourse.group/u/Echelon_Bioanalytics)\ **Replies:** 0\ **Last updated:** [July 4, 2024, 1:36am UTC](https://cwl.discourse.group/t/graphical-user-interface-like-rabix-composer/934 "2024-07-04T01:36:36Z")
Hello, I have been working with Rabix Composer for a while now. It works fine but does not have the functionality to include version 1.1. Also since it is out of development, several bugs are left unattended. I was wond… --- ## [Collect input files by name from directories](https://cwl.discourse.group/t/collect-input-files-by-name-from-directories/932)
**Author:** [@Brilator](https://cwl.discourse.group/u/Brilator)\ **Replies:** 0\ **Last updated:** [July 3, 2024, 2:58pm UTC](https://cwl.discourse.group/t/collect-input-files-by-name-from-directories/932 "2024-07-03T14:58:28Z")
Hi everyone, I’m trying to collect input files for a workflow step from various directories into one directory (as required input for the next step). The files should match a name pattern (i.e. be of a specific file ty… --- ## [.cwl workflow find file in subdirectories of an input directory](https://cwl.discourse.group/t/cwl-workflow-find-file-in-subdirectories-of-an-input-directory/191)
**Author:** [@cccnrc](https://cwl.discourse.group/u/cccnrc)\ **Replies:** 7\ **Last updated:** [July 3, 2024, 7:12am UTC](https://cwl.discourse.group/t/cwl-workflow-find-file-in-subdirectories-of-an-input-directory/191 "2024-07-03T07:12:17Z")
I have output files from a previous step organized as files inside subdirectories of an output directory. Such as: /home/enrico/Dropbox/NY/app/GATK\_CNV\_germline/scatterIntervals/scattered\_hs37d5.preprocessed.300bp.prima… --- ## [How to get input name from a tool parsed using \`cwl\_utils.parser.load\_document\_by\_uri\`](https://cwl.discourse.group/t/how-to-get-input-name-from-a-tool-parsed-using-cwl-utils-parser-load-document-by-uri/922)
**Author:** [@sphuber](https://cwl.discourse.group/u/sphuber)\ **Replies:** 2\ **Last updated:** [July 1, 2024, 10:20am UTC](https://cwl.discourse.group/t/how-to-get-input-name-from-a-tool-parsed-using-cwl-utils-parser-load-document-by-uri/922 "2024-07-01T10:20:41Z")
Hello everyone, I am trying out the cwl\_utils package to parse CWL documents. Consider the following tool.cwl: cwlVersion: v1.0 class: CommandLineTool baseCommand: echo inputs: message: type: string inputBind… --- ## [Cwltool uses docker --mounts](https://cwl.discourse.group/t/cwltool-uses-docker-mounts/929)
**Author:** [@tjvneste](https://cwl.discourse.group/u/tjvneste)\ **Replies:** 1\ **Last updated:** [July 1, 2024, 10:17am UTC](https://cwl.discourse.group/t/cwltool-uses-docker-mounts/929 "2024-07-01T10:17:13Z")
I’m trying to implement tests for my cwl code in bitbucket pipelines. Therefore I need to run the cwl code using: cwltool main.cwl inputs.yml Although this works locally, if you run this in the bitbucket pipeline you g… --- ## [Exploring Job Opportunities in Bioinformatics and CWL Development](https://cwl.discourse.group/t/exploring-job-opportunities-in-bioinformatics-and-cwl-development/923)
**Author:** [@Monika\_Krzyzanowska](https://cwl.discourse.group/u/Monika_Krzyzanowska)\ **Replies:** 1\ **Last updated:** [May 25, 2024, 8:46pm UTC](https://cwl.discourse.group/t/exploring-job-opportunities-in-bioinformatics-and-cwl-development/923 "2024-05-25T20:46:18Z")
I am currently exploring job opportunities in the field of bioinformatics and CWL. I’m eager to connect with companies or individuals who are looking for someone with my skill set. I have background in bioinformatics an… --- ## [CWL - specifying Directory outputs as an input](https://cwl.discourse.group/t/cwl-specifying-directory-outputs-as-an-input/107)
**Author:** [@skanwal](https://cwl.discourse.group/u/skanwal)\ **Replies:** 13\ **Last updated:** [May 15, 2024, 6:55pm UTC](https://cwl.discourse.group/t/cwl-specifying-directory-outputs-as-an-input/107 "2024-05-15T18:55:55Z")
Hello, I am working on a tool definition that requires specifying an input parameter for the outputs location. I have managed to write the following tool definition, that works as expected when testing with cwltool. c… --- ## [How to have configure secondaryFiles to recognize two different patterns for the same file](https://cwl.discourse.group/t/how-to-have-configure-secondaryfiles-to-recognize-two-different-patterns-for-the-same-file/729)
**Author:** [@steve](https://cwl.discourse.group/u/steve)\ **Replies:** 2\ **Last updated:** [May 18, 2024, 8:27pm UTC](https://cwl.discourse.group/t/how-to-have-configure-secondaryfiles-to-recognize-two-different-patterns-for-the-same-file/729 "2024-05-18T20:27:29Z")
We have a lot of legacy systems that output files in a naming format like this; Sample1.bam Sample1.bai And we have some other systems that have the same files named like this; Sample1.bam Sample1.bam.bai I need to a… --- ## [Example CWL FastAPI execution in Python](https://cwl.discourse.group/t/example-cwl-fastapi-execution-in-python/919)
**Author:** [@jzvolensky](https://cwl.discourse.group/u/jzvolensky)\ **Replies:** 2\ **Last updated:** [May 18, 2024, 6:05pm UTC](https://cwl.discourse.group/t/example-cwl-fastapi-execution-in-python/919 "2024-05-18T18:05:07Z")
Hello everyone, I am currently working on a little testing project of creating a smalled dockerized FastAPI service for executing CWL workflows via OGC API. I am storing CWL workflows in an sqlite db and would like to e… --- ## [CWL Working Groups](https://cwl.discourse.group/t/cwl-working-groups/912)
**Author:** [@GlassOfWhiskey](https://cwl.discourse.group/u/GlassOfWhiskey)\ **Replies:** 0\ **Last updated:** [May 13, 2024, 8:31am UTC](https://cwl.discourse.group/t/cwl-working-groups/912 "2024-05-13T08:31:56Z")
Presenter: Iacopo Colonnelli, University of Turino Schedule: Session 5 (Amsterdam / Online hybrid) Thursday 16 May, APAC-EMEA Friendly time This presentation introduces the new CWL Working Groups initiative, describi… --- ## [Invited Keynote: The Pegasus Workflow Management System: Current Applications and Future Directions](https://cwl.discourse.group/t/invited-keynote-the-pegasus-workflow-management-system-current-applications-and-future-directions/915)
**Author:** [@mrc](https://cwl.discourse.group/u/mrc)\ **Replies:** 0\ **Last updated:** [May 15, 2024, 4:32pm UTC](https://cwl.discourse.group/t/invited-keynote-the-pegasus-workflow-management-system-current-applications-and-future-directions/915 "2024-05-15T16:32:55Z")
Presenter: Ewa Deelman Slides: 2024-05-15 CWLCon2024 Invited Keynote: Ewa Deelman The Pegasus Workflow Management System: Current Applications and Future Directions.pdf - Google Drive --- ## [Renku: a platform for sustainable data science](https://cwl.discourse.group/t/renku-a-platform-for-sustainable-data-science/888)
**Author:** [@rokroskar](https://cwl.discourse.group/u/rokroskar)\ **Replies:** 1\ **Last updated:** [May 15, 2024, 2:03pm UTC](https://cwl.discourse.group/t/renku-a-platform-for-sustainable-data-science/888 "2024-05-15T14:03:32Z")
Presenter: Rok Roškar (@rrrrrok@fosstodon.org), Head Of Engineering at Swiss Data Science Center Schedule: Session 4 (Amsterdam / Online hybrid) Wednesday 15 May EMEA Friendly time Sustainability in data-centric res… --- ## [CPU allocation from Slurm](https://cwl.discourse.group/t/cpu-allocation-from-slurm/910)
**Author:** [@tikk3r](https://cwl.discourse.group/u/tikk3r)\ **Replies:** 4\ **Last updated:** [May 13, 2024, 5:21pm UTC](https://cwl.discourse.group/t/cpu-allocation-from-slurm/910 "2024-05-13T17:21:31Z")
I was wondering how cwltool determines how many cores it has available to distribute to jobs. The only bit to go on that I could find was in cwltool/cwltool/executors.py, where I see a reference to psutil.cpu\_count(), bu… --- ## [NGS360 - A NGS Data Management and Analysis Platform](https://cwl.discourse.group/t/ngs360-a-ngs-data-management-and-analysis-platform/893)
**Author:** [@Ryan\_G](https://cwl.discourse.group/u/Ryan_G)\ **Replies:** 0\ **Last updated:** [May 5, 2024, 5:35pm UTC](https://cwl.discourse.group/t/ngs360-a-ngs-data-management-and-analysis-platform/893 "2024-05-05T17:35:04Z")
Presenter: Ryan Golhar, Bristol-Myers Squibb NGS360 is a cloud-based web-enabled platform developed and used at Bristol-Myers Squibb (BMS) to manage NGS data for both research projects and clinical trials across the co… --- ## [Advancing Workflow Automation: Insights from Workflow Execution Service and the Common Workflow Language](https://cwl.discourse.group/t/advancing-workflow-automation-insights-from-workflow-execution-service-and-the-common-workflow-language/876)
**Author:** [@inutano](https://cwl.discourse.group/u/inutano)\ **Replies:** 0\ **Last updated:** [April 24, 2024, 10:38am UTC](https://cwl.discourse.group/t/advancing-workflow-automation-insights-from-workflow-execution-service-and-the-common-workflow-language/876 "2024-04-24T10:38:30Z")
Presenter: Tazro Ohta, Chiba University Session 4 (Amsterdam / Online hybrid) Wednesday 15 May The talk introduced Workflow Execution Service (WES), focusing on its role in automating bioinformatics data processing. … [Previous page](https://cwl.discourse.group/latest.md) [Next page](https://cwl.discourse.group/latest.md?page=2)