# Line of code Training \> nf-core \> part 3 \> 3.5 fails me **URL:** \ **Category:** Training\ **Created:** [April 20, 2026, 8:03pm UTC](https://community.seqera.io/t/line-of-code-training-nf-core-part-3-3-5-fails-me/2639 "2026-04-20T20:03:46Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![m-d-grunnill](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/m-d-grunnill/32/2414_2.png) [@m-d-grunnill](https://community.seqera.io/u/m-d-grunnill)\ **Post date:** [April 20, 2026, 8:03pm UTC](https://community.seqera.io/t/line-of-code-training-nf-core-part-3-3-5-fails-me/2639/1 "2026-04-20T20:03:46Z")
When I run the line `nextflow run . --outdir core-hello-results -profile test,docker --validate_params false` in Training \> nf-core \> part 3 \> 3.5 I get the error: ```auto Nextflow 25.10.4 is available - Please consider updating your version to it N E X T F L O W ~ version 25.10.2 Launching `./main.nf` [suspicious_swartz] DSL2 - revision: b9e9b3b8de Input/output options input : /workspaces/training/hello-nf-core/core-hello/assets/greetings.csv outdir : core-hello-results Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function Generic options validate_params : false trace_report_suffix : 2026-04-20_19-57-37 Core Nextflow options runName : suspicious_swartz containerEngine : docker launchDir : /workspaces/training/hello-nf-core/core-hello workDir : /workspaces/training/hello-nf-core/core-hello/work projectDir : /workspaces/training/hello-nf-core/core-hello userName : root profile : test,docker configFiles : /workspaces/training/hello-nf-core/core-hello/nextflow.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ executor > local (6) [b4/48c9a7] process > CORE_HELLO:HELLO:sayHello (3) [100%] 3 of 3 ✔ [d9/9b3979] process > CORE_HELLO:HELLO:convertToUpper (3) [100%] 3 of 3 ✔ [-] process > CORE_HELLO:HELLO:CAT_CAT - [-] process > CORE_HELLO:HELLO:cowpy - ERROR ~ Error executing process > 'CORE_HELLO:HELLO:CAT_CAT (test)' Caused by: WARNING: This module has been deprecated. Please use nf-core/modules/find/concatenate Reason: This module passes all input files as shell arguments, which can exceed the UNIX ARG_MAX limit when concatenating large numbers of files. The find/concatenate module resolves this by staging files into a directory and enumerating them with `find`, and also enforces consistent input compression (all gzipped or all uncompressed). Also enables faster, parallel decompression with pigz. . Expression: false -- Check script 'modules/nf-core/cat/cat/main.nf' at line: 31 Source block: def deprecation_message = """ WARNING: This module has been deprecated. Please use nf-core/modules/find/concatenate Reason: This module passes all input files as shell arguments, which can exceed the UNIX ARG_MAX executor > local (6) [b4/48c9a7] process > CORE_HELLO:HELLO:sayHello (3) [100%] 3 of 3 ✔ [d9/9b3979] process > CORE_HELLO:HELLO:convertToUpper (3) [100%] 3 of 3 ✔ [-] process > CORE_HELLO:HELLO:CAT_CAT - [-] process > CORE_HELLO:HELLO:cowpy - Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'CORE_HELLO:HELLO:CAT_CAT (test)' Caused by: WARNING: This module has been deprecated. Please use nf-core/modules/find/concatenate Reason: This module passes all input files as shell arguments, which can exceed the UNIX ARG_MAX limit when concatenating large numbers of files. The find/concatenate module resolves this by staging files into a directory and enumerating them with `find`, and also enforces consistent input compression (all gzipped or all uncompressed). Also enables faster, parallel decompression with pigz. . Expression: false -- Check script 'modules/nf-core/cat/cat/main.nf' at line: 31 Source block: def deprecation_message = """ WARNING: This module has been deprecated. Please use nf-core/modules/find/concatenate Reason: This module passes all input files as shell arguments, which can exceed the UNIX ARG_MAX limit when concatenating large numbers of files. The find/concatenate module resolves this by staging files into a directory and enumerating them with `find`, and also enforces consistent input compression (all gzipped or all uncompressed). Also enables faster, parallel executor > local (6) [b4/48c9a7] process > CORE_HELLO:HELLO:sayHello (3) [100%] 3 of 3 ✔ [d9/9b3979] process > CORE_HELLO:HELLO:convertToUpper (3) [100%] 3 of 3 ✔ [-] process > CORE_HELLO:HELLO:CAT_CAT - [-] process > CORE_HELLO:HELLO:cowpy - Execution cancelled -- Finishing pending tasks before exit -[core/hello] Pipeline completed with errors- ERROR ~ Error executing process > 'CORE_HELLO:HELLO:CAT_CAT (test)' Caused by: WARNING: This module has been deprecated. Please use nf-core/modules/find/concatenate Reason: This module passes all input files as shell arguments, which can exceed the UNIX ARG_MAX limit when concatenating large numbers of files. The find/concatenate module resolves this by staging files into a directory and enumerating them with `find`, and also enforces consistent input compression (all gzipped or all uncompressed). Also enables faster, parallel decompression with pigz. . Expression: false -- Check script 'modules/nf-core/cat/cat/main.nf' at line: 31 Source block: def deprecation_message = """ WARNING: This module has been deprecated. Please use nf-core/modules/find/concatenate Reason: This module passes all input files as shell arguments, which can exceed the UNIX ARG_MAX limit when concatenating large numbers of files. The find/concatenate module resolves this by staging files into a directory and enumerating them with `find`, and also enforces consistent input compression (all gzipped or all uncompressed). Also enables faster, parallel decompression with pigz. """ assert false: deprecation_message def file_list = files_in.collect { file -> file.toString() } prefix = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}" Container: quay.io/biocontainers/pigz:2.8 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details ``` ---
**Author:** ![m-d-grunnill](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/m-d-grunnill/32/2414_2.png) [@m-d-grunnill](https://community.seqera.io/u/m-d-grunnill)\ **Post date:** [April 20, 2026, 8:25pm UTC](https://community.seqera.io/t/line-of-code-training-nf-core-part-3-3-5-fails-me/2639/2 "2026-04-20T20:25:20Z")
I solved this problem. I think these were the steps that worked: Step 1: Install find/concatenate in `./core hello/` with `nf-core modules install find/concatenate`. Step 2: Change `core-hello/workflows/hello.nf` contents to: ``` /\* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``` IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ``` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \*/ include { paramsSummaryMap } from ‘plugin/nf-schema’ include { softwareVersionsToYAML } from ‘../subworkflows/nf-core/utils\_nfcore\_pipeline’ include { sayHello } from ‘../modules/local/sayHello.nf’ include { convertToUpper } from ‘../modules/local/convertToUpper.nf’ include { cowpy } from ‘../modules/local/cowpy.nf’ include { FIND\_CONCATENATE } from ‘../modules/nf-core/find/concatenate/main’ /\* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``` RUN MAIN WORKFLOW ``` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \*/ workflow HELLO { ``` take: ch_samplesheet // channel: samplesheet read in from --input main: ch_versions = channel.empty() // emit a greeting sayHello(ch_samplesheet) // convert the greeting to uppercase convertToUpper(sayHello.out) // create metadata map with batch name as the ID def concatenate_meta = \[id: params.batch \] // create a channel with metadata and files in tuple format ch_for_concatenate = convertToUpper.out.collect().map { files -> tuple(concatenate_meta, files) } // concatenate the greetings FIND_CONCATENATE(ch_for_concatenate) // extract the file from the tuple since cowpy doesn't use metadata yet ch_for_cowpy = FIND_CONCATENATE.out.file_out.map{ meta, file -> file } // generate ASCII art of the greetings with cowpy cowpy(ch_for_cowpy, params.character) // // Collate and save software versions // def topic_versions = Channel.topic("versions") .distinct() .branch { entry -> versions_file: entry instanceof Path versions_tuple: true } def topic_versions_string = topic_versions.versions_tuple .map { process, tool, version -> \[process\[process.lastIndexOf(':')+1..-1\], " ${tool}: ${version}" \] } .groupTuple(by:0) .map { process, tool_versions -> tool_versions.unique().sort() "${process}:\\n${tool_versions.join('\\n')}" } softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) .mix(topic_versions_string) .collectFile( storeDir: "${params.outdir}/pipeline_info", name: 'hello_software\_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } emit: cowpy_hellos = cowpy.out versions = ch_versions // channel: \[path(versions.yml) \] ``` } /\* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``` THE END ``` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \*/ ``` ---
**Author:** ![GeraldineVdA](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/geraldinevda/32/178_2.png) [@GeraldineVdA](https://community.seqera.io/u/GeraldineVdA)\ **Post date:** [April 21, 2026, 9:38pm UTC](https://community.seqera.io/t/line-of-code-training-nf-core-part-3-3-5-fails-me/2639/3 "2026-04-21T21:38:48Z")
Hi Martin, thanks for reporting this, I’m going to update the materials accordingly. Nice job solving it yourself! ---
**Author:** ![m-d-grunnill](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/m-d-grunnill/32/2414_2.png) [@m-d-grunnill](https://community.seqera.io/u/m-d-grunnill)\ **Post date:** [April 22, 2026, 1:13pm UTC](https://community.seqera.io/t/line-of-code-training-nf-core-part-3-3-5-fails-me/2639/4 "2026-04-22T13:13:57Z")
I think that was all the steps. Just test it to check I am not missing anything. ---
**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\ **Post date:** [April 29, 2026, 1:14pm UTC](https://community.seqera.io/t/line-of-code-training-nf-core-part-3-3-5-fails-me/2639/5 "2026-04-29T13:14:38Z")
Closed on April 29, 2026, 1:14pm UTC This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.