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 <pfeuffer@informatik.uni-tuebingen.de>

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 <pfeuffer@informatik.uni-tuebingen.de>

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

cff9cba

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

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

8f8b859

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

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

f8dceb8

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

Update nextflow_schema.json

a72b149

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

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

aa64204

Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>

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

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer Mar 25, 2022

jpfeuffer commented Mar 25, 2022

jpfeuffer commented Mar 26, 2022

daichengxin commented Mar 27, 2022

jpfeuffer Mar 25, 2022 •

edited

Major fix #145

Major fix #145

Conversation

daichengxin commented Mar 25, 2022

PR checklist

github-actions bot commented Mar 25, 2022 • edited

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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jpfeuffer commented Mar 26, 2022

daichengxin commented Mar 27, 2022

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github-actions bot commented Mar 25, 2022 •

edited

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

jpfeuffer Mar 25, 2022 •

edited