Add mtbseq workflow #8

Mxrcon · 2024-10-28T13:08:02Z

MTBseq addition

Hey there 👋,

This PR adds

all required mtbseq modules
mtbseq workflows and sub workflows
parameters base configuration as used in mtbseq_nf
test profiles for MTBseq

the module structure follows:

── local
│   ├── mtbseq
│   │   ├── tbamend
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbbwa
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbfull
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbgroups
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbjoin
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tblist
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbpile
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbrefine
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbstats
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   ├── tbstrains
│   │   │   ├── environment.yml
│   │   │   ├── main.nf
│   │   │   └── meta.yml
│   │   └── tbvariants
│   │       ├── environment.yml
│   │       ├── main.nf
│   │       └── meta.yml
│   └── utils
│       └── rename_files.nf

I kindly request for your review @abhi18av and @ycode-sh for proceeding with this work.

PR checklist

Perform tests on the workflow
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

conf/mtbseq-base.config

github-actions · 2024-10-28T15:38:18Z

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

Posted for pipeline commit fcef247

+| ✅ 187 tests passed       |+
!| ❗  41 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in README.md: TODO nf-core:
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in gatk4.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in gatk4.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in gatk4.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in gatk4.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in gatk4.nf: List required Conda package(s).
pipeline_todos - TODO string in gatk4.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in gatk4.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
pipeline_todos - TODO string in gatk4.nf: Where applicable please provide/convert compressed files as input/output
pipeline_todos - TODO string in gatk4.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in gatk4.nf: List additional required output channels/values here
pipeline_todos - TODO string in gatk4.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
pipeline_todos - TODO string in gatk4.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
pipeline_todos - TODO string in gatk4.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
pipeline_todos - TODO string in gatk4.nf: Please replace the example samtools command below with your module's command
pipeline_todos - TODO string in gatk4.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
pipeline_todos - TODO string in gatk4.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ 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: CODE_OF_CONDUCT.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: assets/nf-core-tbanalyzer_logo_light.png
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/images/nf-core-tbanalyzer_logo_light.png
files_exist - File found: docs/images/nf-core-tbanalyzer_logo_dark.png
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: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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-tbanalyzer_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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowTbanalyzer.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-schema plugin
nextflow_config - Config variable found: manifest.name
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: manifest.homePage
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-tbanalyzer_logo_light.png matches the template
files_unchanged - docs/images/nf-core-tbanalyzer_logo_light.png matches the template
files_unchanged - docs/images/nf-core-tbanalyzer_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.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 a matching 'report_comment'.
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.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-10-29 03:18:22

abhi18av · 2024-10-28T15:41:02Z

@Mxrcon the major problem here is related to nf-validation plugin.

In the MTBseq-nf when we initiated the nf-schema plugin was fine but now it has been deprecated in favor of nf-validation.

plugin_includes - Found a nf-validation plugin import in ome/runner/work/tbanalyzer/tbanalyzer/workflows/mtbseqnf.nf, but nf-schema was used in nextflow.config

…he new nf-core template

Mxrcon · 2024-10-28T18:33:20Z

@Mxrcon the major problem here is related to nf-validation plugin.

In the MTBseq-nf when we initiated the nf-schema plugin was fine but now it has been deprecated in favor of nf-validation.

plugin_includes - Found a nf-validation plugin import in ome/runner/work/tbanalyzer/tbanalyzer/workflows/mtbseqnf.nf, but nf-schema was used in nextflow.config

Hmm, just checked it, the port from nf-validation to nf-schema is very straightfoward, just added it and I'll now work into the test of the mtbseq workflow

Mxrcon · 2024-10-29T03:17:31Z

Update after Tests

Hey, I've performed local tests for the latest commits and here are the outputs:

Command executed:

nextflow run main.nf -profile conda -c mtbseq-test.conf --mode mtbseq -resume --mtbseq_parallel

executor >  local (27)
[89/24bbfd] process > NFCORE_TBANALYZER:MTBSEQ_NF:QUALITY_CHECK:RENAME_FILES (4781-04) [100%] 3 of 3 ✔
[66/e79bfd] process > NFCORE_TBANALYZER:MTBSEQ_NF:QUALITY_CHECK:FASTQC (4781-04)       [100%] 3 of 3 ✔
[c7/9408b0] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBBWA (4781-04)        [100%] 3 of 3 ✔
[3a/38d282] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBREFINE (4781-04)     [100%] 3 of 3 ✔
[67/526446] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBPILE (4781-04)       [100%] 3 of 3 ✔
[5f/05673e] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBLIST (4781-04)       [100%] 3 of 3 ✔
[49/2405d7] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBVARIANTS (4781-04)   [100%] 3 of 3 ✔
[8b/cb38bc] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBSTATS (cohort)       [100%] 1 of 1 ✔
[fc/6339ea] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBSTRAINS (cohort)     [100%] 1 of 1 ✔
[e1/c2aa8e] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBJOIN (cohort)        [100%] 1 of 1 ✔
[55/f73876] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBAMEND (cohort)       [100%] 1 of 1 ✔
[9d/39b91d] process > NFCORE_TBANALYZER:MTBSEQ_NF:PARALLEL_MODE:TBGROUPS (cohort)      [100%] 1 of 1 ✔
[00/a543e4] process > NFCORE_TBANALYZER:MTBSEQ_NF:MULTIQC                              [100%] 1 of 1 ✔
-[nf-core/tbanalyzer] Pipeline completed successfully-
Completed at: 28-Oct-2024 20:32:17
Duration    : 2h 16m 43s
CPU hours   : 6.6
Succeeded   : 27

Command Executed:

nextflow run main.nf -profile conda -c mtbseq-test.conf --mode mtbseq -resume

executor >  local (11)
[ea/1186c5] process > NFCORE_TBANALYZER:MTBSEQ_NF:QUALITY_CHECK:RENAME_FILES (3494-04) [100%] 3 of 3 ✔
[de/f3d790] process > NFCORE_TBANALYZER:MTBSEQ_NF:QUALITY_CHECK:FASTQC (3494-04)       [100%] 3 of 3 ✔
[24/281c56] process > NFCORE_TBANALYZER:MTBSEQ_NF:TBFULL (cohort)                      [100%] 1 of 1 ✔
[27/1965c8] process > NFCORE_TBANALYZER:MTBSEQ_NF:TBJOIN (cohort)                      [100%] 1 of 1 ✔
[6d/4c6c3b] process > NFCORE_TBANALYZER:MTBSEQ_NF:TBAMEND (cohort)                     [100%] 1 of 1 ✔
[de/d58589] process > NFCORE_TBANALYZER:MTBSEQ_NF:TBGROUPS (cohort)                    [100%] 1 of 1 ✔
[fe/859eb8] process > NFCORE_TBANALYZER:MTBSEQ_NF:MULTIQC                              [100%] 1 of 1 ✔
-[nf-core/tbanalyzer] Pipeline completed successfully-
Completed at: 28-Oct-2024 23:38:20
Duration    : 3h 5m 54s
CPU hours   : 3.0
Succeeded   : 11

Hope that this is enough for a merge, a I would like to proceed with pipeline documentation in another PR if possible.

@abhi18av, I would like to request a new review on this code before our next sync meet.

Kindly,
Davi

abhi18av

Hi @Mxrcon , thank you for accommodating the change request and also for the end-to-end test for the MTBseq mode. I am going ahead with the merge and then we can focus on local MAGMA modules.

abhi18av · 2024-10-30T10:05:28Z

I have just tried to change the mode to method parameter in 4767064

Mxrcon added 4 commits October 28, 2024 09:43

import the modules from the MTBseq-nf pipeline

0eb0105

import MTBseq-NF workflows [ci skip]

e88a06d

update mtbseq-nf to the newest version [ci skip]

c586331

import the original parameters [ci skip]

a62c1a2

abhi18av reviewed Oct 28, 2024

View reviewed changes

conf/mtbseq-base.config Outdated Show resolved Hide resolved

Mxrcon added 7 commits October 28, 2024 11:27

update modules to nf-core folder structure [ci skip]

ae797fb

update module importation on base workflows [ci skip]

68b1782

add mtbseq-nf references data [ci skip]

9eb6013

add mtbseq_ in front of each mtbseq required parameter [ci skip]

f1a212b

update parameter names on mtbseq workflows [ci skip]

80de62e

add rename files utility module [ci skip]

c4c4981

rename mtbseq base config [ci skip]

9d79b32

Mxrcon marked this pull request as ready for review October 28, 2024 15:11

Mxrcon self-assigned this Oct 28, 2024

Merge branch 'dev' into mtbseq-modules

71a23e3

abhi18av self-requested a review October 28, 2024 15:42

remove the plugin nf-validation and add nf-schemaaccordingly to t…

7f75b10

…he new nf-core template

include the mtbseq_nf workflow inside main.nf

1878438

Mxrcon changed the title ~~Mtbseq modules~~ Add mtbseq workflow Oct 28, 2024

Mxrcon added 2 commits October 28, 2024 23:50

changes after test iteration

8dc8525

adding mtbseq test profiles

fcef247

abhi18av approved these changes Oct 30, 2024

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abhi18av merged commit 4767064 into dev Oct 30, 2024
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abhi18av deleted the mtbseq-modules branch October 30, 2024 09:48

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Add mtbseq workflow #8

Add mtbseq workflow #8

Mxrcon commented Oct 28, 2024 •

edited

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github-actions bot commented Oct 28, 2024 •

edited

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❗ Test warnings:

✅ Tests passed:

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abhi18av commented Oct 28, 2024

Mxrcon commented Oct 28, 2024

Mxrcon commented Oct 29, 2024

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abhi18av commented Oct 30, 2024

Add mtbseq workflow #8

Add mtbseq workflow #8

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Mxrcon commented Oct 28, 2024 • edited Loading

MTBseq addition

PR checklist

github-actions bot commented Oct 28, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

abhi18av commented Oct 28, 2024

Mxrcon commented Oct 28, 2024

Mxrcon commented Oct 29, 2024

Update after Tests

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abhi18av commented Oct 30, 2024

Mxrcon commented Oct 28, 2024 •

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github-actions bot commented Oct 28, 2024 •

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