Major fix #145

daichengxin · 2022-03-25T08:36:36Z

PR checklist

pull

github-actions · 2022-03-25T08:37:49Z

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

Posted for pipeline commit b7603b9

+| ✅ 145 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0'

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config

✅ 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: .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: 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-quantms_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-quantms_logo_light.png
files_exist - File found: docs/images/nf-core-quantms_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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowQuantms.groovy
files_exist - File found: modules.json
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-quantms_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: .travis.yml
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: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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.version
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 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 .svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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
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-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore 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: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (152 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.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' 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'.

Run details

nf-core/tools version 2.3.2
Run at 2022-03-27 07:58:13

conf/modules.config

jpfeuffer · 2022-03-25T09:35:59Z

modules/local/openms/epifany/meta.yml

@@ -15,12 +15,13 @@ input:
      type: file
      description: |
        identification results.
-      pattern: "*.{idXML,consensusXML}"
+      pattern: "*.consensusXML"


No, idxml is fine here, too.

jpfeuffer · 2022-03-25T09:36:31Z

modules/local/openms/epifany/meta.yml

 output:
  - epi_inference:
      type: file
      description: |
        identification results with scored/grouped proteins.
+      pattern: "*.consensusXML"


modules/local/openms/filemerge/meta.yml

jpfeuffer · 2022-03-25T09:55:24Z

nextflow.config


    // Protein FDR options
-    protein_fdr = true


Isn't this always true in our pipeline? So I think this should be removed. Some assumptions in our pipeline might not hold if we set this to false. Might work, but I would not risk it until some user specifically requests it.

nextflow_schema.json

jpfeuffer · 2022-03-25T10:00:01Z

nextflow_schema.json

@@ -690,6 +703,18 @@
                    "fa_icon": "fas fa-list-ol",
                    "help_text": "Infer proteins through:\n\n* 'aggregation'  =  aggregates all peptide scores across a protein (by calculating the maximum) (default)\n* 'bayesian'        =  compute a posterior probability for every protein based on a Bayesian network (i.e. using Epifany)\n* ('percolator' not yet supported)\n\n**Note:** If protein grouping is performed also depends on the `protein_quant` parameter (i.e. if peptides have to be unique or unique to a group only)",
                    "enum": ["aggregation", "bayesian"]
+                },
+                "epifany_debug": {


They should use the same parameter. They are an either/or

this and proteininference

jpfeuffer · 2022-03-25T10:02:21Z

subworkflows/local/phosphoscoring.nf

@@ -13,7 +13,7 @@ workflow PHOSPHOSCORING {
    main:
    ch_version = Channel.empty()

-    IDSCORESWITCHERFORLUCIPHOR(id_files.combine(val("Posterior Error Probability_score")))
+    IDSCORESWITCHERFORLUCIPHOR(id_files.combine(Channel.value("\"Posterior Error Probability\"")))


was this change tested? you can use the new uploaded test data.

jpfeuffer · 2022-03-25T10:02:31Z

subworkflows/local/phosphoscoring.nf

@@ -13,7 +13,7 @@ workflow PHOSPHOSCORING {
    main:
    ch_version = Channel.empty()

-    IDSCORESWITCHERFORLUCIPHOR(id_files.combine(val("Posterior Error Probability_score")))
+    IDSCORESWITCHERFORLUCIPHOR(id_files.combine(Channel.value("\"Posterior Error Probability\"")))


was this change tested? you can use the new uploaded test data.

Co-authored-by: Julianus Pfeuffer <[email protected]>

jpfeuffer · 2022-03-25T11:33:11Z

Linting still fails. You might be able to just do prettier -m if you have prettier installed.

jpfeuffer · 2022-03-26T10:34:23Z

Nice. How did you fix the testdata?

daichengxin · 2022-03-27T06:21:20Z

Without fixing test_localize testdata .Network issues?

jpfeuffer · 2022-03-25T13:50:57Z

conf/test_localize.config

+    max_time = 1.h
+
+    // Input data
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/phospho/test_phospho.sdrf'


I copied everything to the quantms branch, too. We can do that later.

daichengxin and others added 2 commits March 25, 2022 13:04

Merge pull request #1 from bigbio/dev

bd2adf2

pull

Major fix

e83ef1a

fixed

58bc938

jpfeuffer requested changes Mar 25, 2022

View reviewed changes

daichengxin and others added 6 commits March 25, 2022 18:13

Update modules/local/openms/filemerge/meta.yml

182da7d

Co-authored-by: Julianus Pfeuffer <[email protected]>

Update modules/local/openms/filemerge/meta.yml

cff9cba

Co-authored-by: Julianus Pfeuffer <[email protected]>

Update modules/local/openms/thirdparty/luciphoradapter/main.nf

8f8b859

Co-authored-by: Julianus Pfeuffer <[email protected]>

Update modules/local/openms/thirdparty/luciphoradapter/meta.yml

f8dceb8

Co-authored-by: Julianus Pfeuffer <[email protected]>

Update nextflow_schema.json

a72b149

Co-authored-by: Julianus Pfeuffer <[email protected]>

Update modules/local/openms/thirdparty/luciphoradapter/meta.yml

aa64204

Co-authored-by: Julianus Pfeuffer <[email protected]>

daichengxin added 4 commits March 25, 2022 21:34

fixed

b7f27cd

fixed

c3770e2

update testdata url

57bd941

update testdata

d2e8545

daichengxin added 2 commits March 27, 2022 15:52

fixed diann bug

1e4784e

fix lint

b7603b9

daichengxin mentioned this pull request Mar 27, 2022

Since DIA-NN is not supported by conda, not the entire pipeline no #136

Closed

ypriverol linked an issue Mar 27, 2022 that may be closed by this pull request

Since DIA-NN is not supported by conda, not the entire pipeline no #136

Closed

jpfeuffer approved these changes Mar 27, 2022

View reviewed changes

jpfeuffer merged commit eb8ee5d into bigbio:dev Mar 27, 2022

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Major fix #145

Major fix #145

daichengxin commented Mar 25, 2022

github-actions bot commented Mar 25, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

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jpfeuffer commented Mar 25, 2022

jpfeuffer commented Mar 26, 2022

daichengxin commented Mar 27, 2022

jpfeuffer Mar 25, 2022 •

edited

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Major fix #145

Major fix #145

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daichengxin commented Mar 25, 2022

PR checklist

github-actions bot commented Mar 25, 2022 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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

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