enforce style and add aws test #186

daichengxin · 2022-05-20T07:07:22Z

PR checklist

github-actions · 2022-05-20T07:08:48Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit ae198ce

+| ✅ 146 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: conf/test.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: 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: .nf-core.yaml
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 .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '1.1dev'
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 (170 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.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 2.4.1
Run at 2022-05-23 12:03:39

u

bin/diann_convert.py

modules/local/diannconvert/main.nf

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

jpfeuffer · 2022-05-23T19:23:41Z

bin/diann_convert.py

@@ -47,7 +52,10 @@ def convert(ctx, diann_report, exp_design):
    out_triqler = pd.DataFrame()
    out_triqler = out_msstats[['ProteinName', 'PeptideSequence', 'PrecursorCharge', 'Intensity', 'Run', 'Condition']]
    out_triqler.columns = ['proteins', 'peptide', 'charge', 'intensity', 'run', 'condition']
-    out_triqler.loc[:, "searchScore"] = 1 - report['PEP']
+
+    # https://github.com/statisticalbiotechnology/dia_sum/blob/main/scripts/result_scripts/diann_output_to_triqler_output.py


This does not apply anymore.

jpfeuffer · 2022-05-23T19:24:06Z

conf/test_full_dia.config

+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running real full dia tests (DIA)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.


Not fast and simple

jpfeuffer · 2022-05-23T19:25:48Z

conf/test_full_lfq.config

+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running real full-size tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.


Not fast and simple

jpfeuffer · 2022-05-23T19:27:41Z

modules/local/diannsummary/main.nf

@@ -41,6 +44,7 @@ process DIANNSUMMARY {
            --use-quant \\
            --matrices \\
            --out diann_report.tsv \\
+            --qvalue $params.psm_level_fdr_cutoff \\


I thought the final output are proteins?

jpfeuffer · 2022-05-23T19:29:50Z

@ypriverol I found some minor doc errors and wrong FDR parameter.

enforce style and add aws test

0c0152a

daichengxin and others added 8 commits May 20, 2022 15:55

add dia aws test

777d6ef

add fdr threshold

d9e2a8b

resolve conflict?

8463abe

resolve conflict11

ba5d6fa

conflict

7bc483c

Merge pull request #10 from bigbio/dev

cf598ac

u

remove redundant para

2ffd24a

rename

30b1ea9

jpfeuffer reviewed May 23, 2022

View reviewed changes

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bin/diann_convert.py Outdated Show resolved Hide resolved

modules/local/diannconvert/main.nf Outdated Show resolved Hide resolved

daichengxin and others added 4 commits May 23, 2022 15:45

Update bin/diann_convert.py

cec5bae

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

update

511d183

fixed

e38dfec

Update diann_convert.py

ae198ce

ypriverol linked an issue May 23, 2022 that may be closed by this pull request

DIANN output with Triqler search engine score #188

Closed

ypriverol self-requested a review May 23, 2022 12:53

ypriverol approved these changes May 23, 2022

View reviewed changes

ypriverol merged commit 5fd2dfd into bigbio:dev May 23, 2022

jpfeuffer requested changes May 23, 2022

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enforce style and add aws test #186

enforce style and add aws test #186

daichengxin commented May 20, 2022

github-actions bot commented May 20, 2022 •

edited

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❔ Tests ignored:

✅ Tests passed:

Run details

jpfeuffer May 23, 2022

jpfeuffer May 23, 2022

jpfeuffer May 23, 2022

jpfeuffer May 23, 2022

jpfeuffer commented May 23, 2022

enforce style and add aws test #186

enforce style and add aws test #186

Conversation

daichengxin commented May 20, 2022

PR checklist

github-actions bot commented May 20, 2022 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

jpfeuffer May 23, 2022

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jpfeuffer commented May 23, 2022

github-actions bot commented May 20, 2022 •

edited

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`nf-core lint` overall result: Passed ✅