Add `sample_name` column in samplesheet compatibility #19

sgsutcliffe · 2024-11-06T21:31:34Z

Modified the template for input samplesheet.csv file to include the sample_name column in addition to sample in-line with changes to IRIDA-Next update as seen with the speciesabundance pipeline and staramrnf. What this means is that the output files and the sample name will be changed to sample_name if a sample_name is called. If ftechdatairidanext is being locally then the sample_name can be left blank.

Made a few changes:
- If sample_name is provided it will be prefixed to reads file name
- If sample_name is provided it will also be included in failure report (if generated)

PR checklist

sgsutcliffe · 2024-11-06T21:36:51Z

SOLVED

Wanted to push the changes to see if an issue I had testing locally would be replicated. It looks like there is an issue with fasterq-dump possibly prefetch where the command.sh runs, and running the command via nextflow run main.nf works for test("Include sample_name in samplesheet") .

sgsutcliffe · 2024-11-07T19:30:59Z

It turns out the issue was with fasterq-dump. The issue is documented here and the solution is to roll back the version of fasterq-dump. As was done for fetchngs PR 261.

github-actions · 2024-11-07T19:51:53Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 1238b14

+| ✅ 126 tests passed       |+
#| ❔  32 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes_ignored.config
nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
nextflow_config - Config manifest.version should end in dev: 1.2.0
schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/fetchdatairidanext/master/nextflow_schema.json
Found https://raw.githubusercontent.com/phac-nml/fetchdatairidanext/main/nextflow_schema.json
nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-fetchdatairidanext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-fetchdatairidanext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-fetchdatairidanext_logo_dark.png
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/NfcoreTemplate.groovy
files_exist - File is ignored: lib/WorkflowFetchdatairidanext.groovy
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: params.max_cpus
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-fetchdatairidanext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-fetchdatairidanext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-fetchdatairidanext_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchdatairidanext/fetchdatairidanext/.github/workflows/awstest.yml
actions_awsfulltest - actions_awsfulltest
pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-fetchdatairidanext_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-validation plugin
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.rename_with_samplename= true
nextflow_config - Config default value correct: params.max_cpus= 4
nextflow_config - Config default value correct: params.max_memory= 2.GB
nextflow_config - Config default value correct: params.max_time= 1.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.max_jobs_with_network_connections= 1
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - SRATOOLS_PREFETCH found in conf/modules.config and Nextflow scripts.
modules_config - SRATOOLS_FASTERQDUMP found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

nf-core/tools version 3.0.2
Run at 2024-11-15 15:06:54

…r sample_name

sgsutcliffe · 2024-11-14T21:34:33Z

It's working in IRIDA-Next and the parameter is working!

Example

Add sample_name test is still not working locally

c964c80

sgsutcliffe added 3 commits November 7, 2024 14:37

Fixes isses with fasterq-dump

101bbe5

Added another test, test read names with sample_names

5185a75

Fix nfcore lint issues

46bb5fa

sgsutcliffe added 12 commits November 7, 2024 15:10

Modified linting with editorconfig-checker

0849cc7

Fix lint comment yml

28fa88f

Providing a NCBI user setting file for tests

f025b1b

Providing a NCBI user setting file for tests

201d5e4

Somewhere along the way prefetch got deleted

b55683d

Add sample_name removal of non-alphanumeric characters and nf-test fo…

9e1e92a

…r sample_name

update documenantation, and param to override sample_name rename

d6093db

Update usage.md

f1a50f3

Add new param to schema

0dd868a

Updating UI for IRIDA-Next

8206458

Made it pretty

c877cd4

Improved description for IRIDA-Next parameter

86bccf9

Update version for minor release

1238b14

sgsutcliffe requested review from apetkau, emarinier and kylacochrane November 15, 2024 15:20

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Add `sample_name` column in samplesheet compatibility #19

Add `sample_name` column in samplesheet compatibility #19

sgsutcliffe commented Nov 6, 2024 •

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sgsutcliffe commented Nov 7, 2024

github-actions bot commented Nov 7, 2024 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

sgsutcliffe commented Nov 14, 2024

Add sample_name column in samplesheet compatibility #19

Are you sure you want to change the base?

Add sample_name column in samplesheet compatibility #19

Conversation

sgsutcliffe commented Nov 6, 2024 • edited Loading

PR checklist

sgsutcliffe commented Nov 6, 2024 • edited Loading

SOLVED

sgsutcliffe commented Nov 7, 2024

github-actions bot commented Nov 7, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

sgsutcliffe commented Nov 14, 2024

Example

Add `sample_name` column in samplesheet compatibility #19

Add `sample_name` column in samplesheet compatibility #19

sgsutcliffe commented Nov 6, 2024 •

edited

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sgsutcliffe commented Nov 6, 2024 •

edited

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github-actions bot commented Nov 7, 2024 •

edited

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️