Add Seqera Studios configuration for training environment by ewels · Pull Request #803 · nextflow-io/training

ewels · 2026-02-02T09:49:01Z

No description provided.

netlify · 2026-02-02T09:49:07Z

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github-actions · 2026-02-02T09:49:53Z

Nextflow linting complete!

✅ 171 files had no errors
🔧 127 files would be changed by auto-formatting

View formatting changes

File	Diff
hello-nextflow/solutions/1-hello-world/hello-world-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - output: path 'output.txt'
hello-nextflow/solutions/1-hello-world/hello-world-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,7 +28,7 @@ workflow { main: // create a channel for inputs greeting_ch = channel.of('Hello Channels!') - .view() + .view() // emit a greeting ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,7 +28,7 @@ workflow { main: // create a channel for inputs greeting_ch = channel.of('Hello', 'Bonjour', 'Holà') - .view() + .view() // emit a greeting ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -28,12 +27,12 @@ workflow { main: // declare an array of input greetings - greetings_array = ['Hello','Bonjour','Holà'] + greetings_array = ['Hello', 'Bonjour', 'Holà'] // create a channel for inputs ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,11 +28,11 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .view { csv -> "Before splitCsv: $csv" } - .splitCsv() - .view { csv -> "After splitCsv: $csv" } ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf	View @@ -7,7 +7,6 @@ include { sayHello } from './modules/sayHello.nf' * Use a text replacement tool to convert the greeting to uppercase / process convertToUpper { - input: path input_file @@ -24,7 +23,6 @@ process convertToUpper { Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf	View @@ -8,7 +8,6 @@ include { convertToUpper } from './modules/convertToUpper.nf' * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name @@ -38,8 +37,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf	View @@ -18,8 +18,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf	View @@ -2,7 +2,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf	View @@ -2,7 +2,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf	View @@ -20,8 +20,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/5-hello-containers/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/5-hello-containers/modules/convertToUpper.nf	View @@ -2,7 +2,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/5-hello-containers/modules/sayHello.nf	View @@ -2,7 +2,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/6-hello-config/hello-config.nf	View @@ -20,8 +20,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/6-hello-config/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/6-hello-config/modules/convertToUpper.nf	View @@ -2,7 +2,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/6-hello-config/modules/sayHello.nf	View @@ -2,7 +2,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/6-hello-config/nextflow.config	View @@ -6,7 +6,7 @@ conda.enabled = true */ process { memory = 1.GB - withName: 'cowpy' { + withName: cowpy { memory = 2.GB cpus = 2 } @@ -32,11 +32,7 @@ profiles { univ_hpc { process.executor = 'slurm' conda.enabled = true - process.resourceLimits = [ - memory: 750.GB, ... (truncated)
hello-nf-core/solutions/composable-hello/hello.nf	View @@ -14,9 +14,7 @@ include { collectGreetings } from './modules/collectGreetings.nf' include { cowpy } from './modules/cowpy.nf' workflow HELLO { - take: - // channel of greetings greeting_ch main:
hello-nf-core/solutions/composable-hello/main.nf	View @@ -9,12 +9,12 @@ params.greeting = 'greetings.csv' workflow { // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.greeting) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // call the imported workflow on the channel of greetings HELLO(greeting_ch) // view the outputs emitted by the workflow - HELLO.out.view { output -> "Output: $output" } + HELLO.out.view { output -> "Output: ${output}" } ... (truncated)
hello-nf-core/solutions/composable-hello/modules/collectGreetings.nf	View @@ -10,8 +10,8 @@ process collectGreetings { val batch_name output: - path "COLLECTED-${batch_name}-output.txt" , emit: outfile - val count_greetings , emit: count + path "COLLECTED-${batch_name}-output.txt", emit: outfile + val count_greetings, emit: count script: count_greetings = input_files.size()
hello-nf-core/solutions/composable-hello/modules/convertToUpper.nf	View @@ -13,6 +13,6 @@ process convertToUpper { script: """ - cat '$input_file' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + cat '${input_file}' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' """ }
hello-nf-core/solutions/composable-hello/modules/cowpy.nf	View @@ -15,6 +15,6 @@ process cowpy { script: """ - cat $input_file \| cowpy -c "$character" > cowpy-${input_file} + cat ${input_file} \| cowpy -c "${character}" > cowpy-${input_file} """ }
hello-nf-core/solutions/composable-hello/modules/sayHello.nf	View @@ -13,6 +13,6 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo '${greeting}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/conf/base.config	View @@ -11,13 +11,13 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' + maxRetries = 1 ... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/modules.config	View @@ -12,10 +12,5 @@ process { - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - + publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] }
hello-nf-core/solutions/core-hello-part2/conf/test.config	View @@ -11,21 +11,17 @@ */ process { - resourceLimits = [ - cpus: 2, - memory: '4.GB', - time: '1.h' - ] + resourceLimits = [cpus: 2, memory: '4.GB', time: '1.h'] } params { - config_profile_name = 'Test profile' + config_profile_name = 'Test profile' ... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/test_full.config	View @@ -11,7 +11,7 @@ */ params { - config_profile_name = 'Full test profile' + config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test
hello-nf-core/solutions/core-hello-part2/main.nf	View @@ -13,9 +13,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ / -include { HELLO } from './workflows/hello' +include { HELLO } from './workflows/hello' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_hello_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' / ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -26,7 +26,6 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hell // WORKFLOW: Run main analysis pipeline depending on type of input // ... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/collectGreetings.nf	View @@ -10,8 +10,8 @@ process collectGreetings { val batch_name output: - path "COLLECTED-${batch_name}-output.txt" , emit: outfile - val count_greetings , emit: count + path "COLLECTED-${batch_name}-output.txt", emit: outfile + val count_greetings, emit: count script: count_greetings = input_files.size()
hello-nf-core/solutions/core-hello-part2/modules/local/convertToUpper.nf	View @@ -13,6 +13,6 @@ process convertToUpper { script: """ - cat '$input_file' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + cat '${input_file}' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' """ }
hello-nf-core/solutions/core-hello-part2/modules/local/cowpy.nf	View @@ -7,14 +7,14 @@ process cowpy { conda 'conda-forge::cowpy==1.1.5' input: - path input_file - val character + path input_file + val character output: - path "cowpy-${input_file}" + path "cowpy-${input_file}" script: """ ... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/sayHello.nf	View @@ -13,6 +13,6 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo '${greeting}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/nextflow.config	View @@ -11,30 +11,30 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options - input = null + input = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - monochrome_logs = false - help = false - help_full = false - show_hidden = false - version = false ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf	View @@ -8,13 +8,13 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' -include { paramsHelp } from 'plugin/nf-schema' -include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf	View @@ -10,9 +10,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { take: - print_version // boolean: print version - dump_parameters // boolean: dump parameters - outdir // path: base directory used to publish pipeline results + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results check_conda_channels // boolean: check conda channels main: @@ -72,10 +72,10 @@ def getWorkflowVersion() { // ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config	View @@ -1,9 +1,9 @@ manifest { - name = 'nextflow_workflow' - author = """nf-core""" - homePage = 'https://127.0.0.1' - description = """Dummy pipeline""" + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" nextflowVersion = '!>=23.04.0' - version = '9.9.9' - doi = 'https://doi.org/10.5281/zenodo.5070524' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf	View @@ -125,12 +125,12 @@ def paramsSummaryMultiqc(summary_params) { } def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: \|\n" - yaml_file_text += "${summary_section}" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: \|\n" ... (truncated)
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hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfschema_plugin/main.nf	(truncated)
hello-nf-core/solutions/core-hello-start/workflows/hello.nf	(truncated)
nextflow-run/solutions/3-main.nf	(truncated)
nextflow-run/solutions/modules/collectGreetings.nf	(truncated)
nextflow-run/solutions/modules/convertToUpper.nf	(truncated)
nextflow-run/solutions/modules/sayHello.nf	(truncated)
nextflow-run/solutions/nextflow.config	(truncated)
side-quests/solutions/debugging/buggy_workflow.nf	(truncated)
side-quests/solutions/essential_scripting_patterns/main.nf	(truncated)

ewels · 2026-02-02T10:55:43Z

Sadly seems that docker-in-docker is still problematic in Studios:

Example Nextflow CLI output with error

root@ip-172-31-40-73:~/training/hello-nextflow# nextflow run solutions/5-hello-containers/hello-containers-2.nf -c solutions/5-hello-containers/nextflow.config 
Nextflow 25.10.3 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 25.10.2

Launching `solutions/5-hello-containers/hello-containers-2.nf` [silly_davinci] DSL2 - revision: 7fb7d4ac03

executor >  local (8)
[c3/e4267e] process > sayHello (2)       [100%] 3 of 3 ✔
[12/eba44b] process > convertToUpper (3) [100%] 3 of 3 ✔
[7e/2f1416] process > collectGreetings   [100%] 1 of 1 ✔
[75/4b73aa] process > cowpy              [  0%] 0 of 1
ERROR ~ Error executing process > 'cowpy'

Caused by:
  Process `cowpy` terminated with an error exit status (125)


Command executed:

  cat COLLECTED-batch-output.txt | cowpy -c "turkey" > cowpy-COLLECTED-batch-output.txt

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273' locally
  1.1.5--3db457ae1977a273: Pulling from library/cowpy
  dafa2b0c44d2: Pulling fs layer
  f88da01cff0b: Pulling fs layer
  92dc97a3ef36: Pulling fs layer
  4f4fb700ef54: Pulling fs layer
  403f74b0f85e: Pulling fs layer
  0ea1a16bbe82: Pulling fs layer
  dec6b097362e: Pulling fs layer
  17dc7ea432cc: Pulling fs layer
  10b8c00c10a5: Pulling fs layer
  4f4fb700ef54: Pulling fs layer
  030a47592a0a: Pulling fs layer
  e1686ff32a11: Pulling fs layer
  c23bdb422167: Pulling fs layer
  bb36d6c3110d: Pulling fs layer
  403f74b0f85e: Download complete
  f88da01cff0b: Download complete
  4f4fb700ef54: Download complete
  bb36d6c3110d: Download complete
  030a47592a0a: Download complete
  dec6b097362e: Download complete
  92dc97a3ef36: Download complete
  0ea1a16bbe82: Download complete
  17dc7ea432cc: Download complete
  10b8c00c10a5: Download complete
  c23bdb422167: Download complete
  dafa2b0c44d2: Download complete
  e1686ff32a11: Download complete
  dec6b097362e: Pull complete
  dafa2b0c44d2: Pull complete
  403f74b0f85e: Pull complete
  f88da01cff0b: Pull complete
  4f4fb700ef54: Pull complete
  bb36d6c3110d: Pull complete
  92dc97a3ef36: Pull complete
  17dc7ea432cc: Pull complete
  10b8c00c10a5: Pull complete
  030a47592a0a: Pull complete
  0ea1a16bbe82: Pull complete
  c23bdb422167: Pull complete
  e1686ff32a11: Pull complete
  Digest: sha256:1ebc0043e8cafa61203bf42d29fd05bd14e7b4298e5e8cf986504c15f5aa4160
  Status: Downloaded newer image for community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273
  docker: Error response from daemon: failed to mount /tmp/containerd-mount2111467694: mount source: "overlay", target: "/tmp/containerd-mount2111467694", fstype: overlay, flags: 0, data: "workdir=/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/15/work,upperdir=/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/15/fs,lowerdir=/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/14/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/13/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/12/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/11/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/10/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/9/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/8/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/7/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/6/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/5/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/4/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/3/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/2/fs:/var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.overlayfs/snapshots/1/fs,index=off", err: invalid argument
  
  Run 'docker run --help' for more information

Work dir:
  /workspace/training/hello-nextflow/work/75/4b73aa65b79bacccefa14b265b5999

Container:
  community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
ERROR ~ Cannot access first() element from an empty List

 -- Check '.nextflow.log' file for details

…kip ci] The base Studios image (data-studio-vscode) ships micromamba but not the `conda` CLI. Nextflow's `conda` directive defaults to invoking `conda`, which fails with "command not found" on processes that declare a conda package (e.g. cowpy in hello_nextflow lesson 6). Setting NXF_HOME to a path that contains a Studios-only config file lets Nextflow auto-load `conda.useMicromamba = true` from `$NXF_HOME/config`. This isolates the override to Studios: Codespaces sets its own NXF_HOME and never sees this file, and local runs use the default `~/.nextflow`. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

- Add `conda` to environment.yaml so Nextflow's `conda` directive can resolve packages (the Studios base image ships micromamba but not the `conda` CLI). Supersedes the .seqera/nxf/config micromamba workaround, which is now removed. - Add `tree` to environment.yaml (handy for learners inspecting layouts). - Remove computeRequirements block so the compute environment can be selected at launch rather than pinned to AWS Batch 8 CPU / 32 GB. - Bump base template image to 1.101.2-0.12 (current production). - Restore NXF_HOME to /workspace/.nextflow now that the micromamba override is no longer needed. The conda + tree additions and the computeRequirements removal are adopted from #897 (FriederikeHanssen). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

pinin4fjords · 2026-05-11T16:27:40Z

Just pushed two commits to studios that draw on @FriederikeHanssen's #897:

12d72f027 + 1ed64df62 combined:

Add tree to environment.yaml — useful for learners (from Update studio config for training #897).
Remove the computeRequirements block — lets the compute environment be selected at launch rather than hard-pinning to AWS Batch 8 CPU / 32 GB (from Update studio config for training #897).
Bump base image to public.cr.seqera.io/platform/data-studio-vscode:1.101.2-0.12 (current production).
NXF_HOME=/workspace/training/.seqera/nxf + ship a one-line .seqera/nxf/config with conda.useMicromamba = true. The base image already provides micromamba; this tells Nextflow to use it for any process that has a conda directive (e.g. cowpy in hello_nextflow lesson 6), without needing the conda CLI on PATH. Verified end-to-end on a stage VM.

On the conda question: #897 had added the full conda package to environment.yaml to give Nextflow's conda directive a CLI to shell out to. I initially cherry-picked that and then reverted it — the base image already ships micromamba, so installing conda on top is ~200 MB of redundant tooling. The NXF_HOME-pointed config file route uses what's already there.

The remaining open item from #897: she had bumped to cr.seqera.io/public/data-studio-vscode:1.101.2-0.10-rc (dev/rc registry). I went with production 1.101.2-0.12 instead. Happy to switch if there's a specific reason to use rc.

Other things in #897 (translations, claude skills updates, scripts) appear unrelated to the Studios config and look like base-branch drift rather than intentional changes — left those out.

The base Studios image already ships micromamba at /bin/micromamba, so installing the full conda package (~200 MB) just to give Nextflow's `conda` directive a CLI to shell out to is wasteful. Revert to pointing NXF_HOME at .seqera/nxf/ and shipping a one-line config file (`conda.useMicromamba = true`). This tells Nextflow to use the already-installed micromamba binary. Only loaded when NXF_HOME is set to this path (Studios only); Codespaces and local checkouts use a different NXF_HOME and never see the file. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Base automatically changed from lang to master February 2, 2026 23:30

ewels added 4 commits March 31, 2026 12:47

Add Seqera Studios configuration for training environment

3794633

Fix environment.yaml path to be relative to .seqera directory

6d4d2e9

Remove Python version pin to fix conda dependency resolution

b0f57e2

Remove openjdk dependency (provided by base image)

5284479

ewels force-pushed the studios branch from 61ccee6 to 5284479 Compare March 31, 2026 10:47

pinin4fjords and others added 2 commits May 11, 2026 16:48

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Add Seqera Studios configuration for training environment#803

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