Get latest dev version to check no flaky bam filtering by jfy133 · Pull Request #556 · nf-core/eager

jfy133 · 2020-09-15T06:29:40Z

nf-core/eager pull request

Many thanks for contributing to nf-core/eager!

Please fill in the appropriate checklist below (delete whatever is not relevant).
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PR checklist

This comment contains a description of changes (with reason)
If you've fixed a bug or added code that should be tested, add tests!
If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
Ensure the test suite passes (nextflow run . -profile test,docker --paired_end).
Make sure your code lints (nf-core lint .).
Documentation in docs is updated
CHANGELOG.md is updated
README.md is updated

Learn more about contributing: CONTRIBUTING.md

syncing

… everything

…cs-schema-update

Tsv headername validation

Docs and schema update

Add bam filtering on fragment length script

Get final python script version

Replaced awk with python version of read filtering

Timelimit mods

github-actions · 2020-09-15T06:38:37Z

`nf-core lint` overall result: Passed ✅

Updated for pipeline commit c2ad7a7

+| ✅ 145 tests passed       |+
!| ❗ 14 tests had warnings |!
-| ❌  0 tests failed       |-

Details

❗ Test warnings:

Test #8 - Conda package is not latest available: conda-forge::python=3.7.3, 3.8.5 available
Test #8 - Conda package is not latest available: conda-forge::pymdown-extensions=7.1, 8.0 available
Test #8 - Conda package is not latest available: conda-forge::pygments=2.6.1, 2.7.0 available
Test #8 - Conda package is not latest available: conda-forge::openjdk=8.0.144, 11.0.8 available
Test #8 - Conda package is not latest available: bioconda::picard=2.22.9, 2.23.4 available
Test #8 - Conda package is not latest available: bioconda::samtools=1.9, 1.10 available
Test #8 - Conda package is not latest available: bioconda::gatk4=4.1.7.0, 4.1.8.1 available
Test #8 - Conda package is not latest available: bioconda::damageprofiler=0.4.9, 0.5.0 available
Test #8 - Conda package is not latest available: conda-forge::libiconv=1.15, 1.16 available
Test #8 - Conda package is not latest available: pysam=0.15.4, 0.16.0.1 available
Test #8 - Conda package is not latest available: conda-forge::pandas=1.0.4, 1.1.2 available
Test #8 - Conda package is not latest available: conda-forge::biopython=1.76, 1.78 available
Test #15 - Schema param awsqueue not found from nextflow config
Test #15 - Schema param awsregion not found from nextflow config

✅ Tests passed:

Test #1 - File found: nextflow.config
Test #1 - File found: nextflow_schema.json
Test #1 - File found: Dockerfile
Test #1 - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
Test #1 - File found: README.md
Test #1 - File found: CHANGELOG.md
Test #1 - File found: docs/README.md
Test #1 - File found: docs/output.md
Test #1 - File found: docs/usage.md
Test #1 - File found: .github/workflows/branch.yml
Test #1 - File found: .github/workflows/ci.yml
Test #1 - File found: .github/workflows/linting.yml
Test #1 - File found: main.nf
Test #1 - File found: environment.yml
Test #1 - File found: conf/base.config
Test #1 - File found: .github/workflows/awstest.yml
Test #1 - File found: .github/workflows/awsfulltest.yml
Test #1 - File not found check: Singularity
Test #1 - File not found check: parameters.settings.json
Test #1 - File not found check: .travis.yml
Test #3 - Licence check passed
Test #2 - Dockerfile check passed
Test #4 - Config variable found: manifest.name
Test #4 - Config variable found: manifest.nextflowVersion
Test #4 - Config variable found: manifest.description
Test #4 - Config variable found: manifest.version
Test #4 - Config variable found: manifest.homePage
Test #4 - Config variable found: timeline.enabled
Test #4 - Config variable found: trace.enabled
Test #4 - Config variable found: report.enabled
Test #4 - Config variable found: dag.enabled
Test #4 - Config variable found: process.cpus
Test #4 - Config variable found: process.memory
Test #4 - Config variable found: process.time
Test #4 - Config variable found: params.outdir
Test #4 - Config variable found: params.input
Test #4 - Config variable found: manifest.mainScript
Test #4 - Config variable found: timeline.file
Test #4 - Config variable found: trace.file
Test #4 - Config variable found: report.file
Test #4 - Config variable found: dag.file
Test #4 - Config variable found: process.container
Test #4 - Config variable (correctly) not found: params.version
Test #4 - Config variable (correctly) not found: params.nf_required_version
Test #4 - Config variable (correctly) not found: params.container
Test #4 - Config variable (correctly) not found: params.singleEnd
Test #4 - Config variable (correctly) not found: params.igenomesIgnore
Test #4 - Config timeline.enabled had correct value: true
Test #4 - Config report.enabled had correct value: true
Test #4 - Config trace.enabled had correct value: true
Test #4 - Config dag.enabled had correct value: true
Test #4 - Config manifest.name began with nf-core/
Test #4 - Config variable manifest.homePage began with https://github.com/nf-core/
Test #4 - Config dag.file ended with .svg
Test #4 - Config variable manifest.nextflowVersion started with >= or !>=
Test #4 - Config process.container looks correct: nfcore/eager:dev
Test #4 - Config manifest.version ends in dev: '2.2.0dev'
Test #5 - GitHub Actions 'branch' workflow is triggered for PRs to master: /home/runner/work/eager/eager/.github/workflows/branch.yml
Test #5 - GitHub Actions 'branch' workflow looks good: /home/runner/work/eager/eager/.github/workflows/branch.yml
Test #5 - GitHub Actions CI is triggered on expected events: /home/runner/work/eager/eager/.github/workflows/ci.yml
Test #5 - CI is building the correct docker image: docker build --no-cache . -t nfcore/eager:dev
Test #5 - CI is pulling the correct docker image: docker pull nfcore/eager:dev
Test #5 - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:dev
Test #5 - Continuous integration checks minimum NF version: /home/runner/work/eager/eager/.github/workflows/ci.yml
Test #5 - GitHub Actions linting workflow is triggered on PR and push: /home/runner/work/eager/eager/.github/workflows/linting.yml
Test #5 - Continuous integration runs Markdown lint Tests: /home/runner/work/eager/eager/.github/workflows/linting.yml
Test #5 - Continuous integration runs nf-core lint Tests: /home/runner/work/eager/eager/.github/workflows/linting.yml
Test #5 - GitHub Actions AWS test is triggered on push and not PRs: /home/runner/work/eager/eager/.github/workflows/awstest.yml
Test #5 - GitHub Actions AWS test is triggered only on push to master: /home/runner/work/eager/eager/.github/workflows/awstest.yml
Test #5 - GitHub Actions AWS full test is triggered only on published release: /home/runner/work/eager/eager/.github/workflows/awsfulltest.yml
Test #5 - GitHub Actions AWS full test should test full datasets: /home/runner/work/eager/eager/.github/workflows/awsfulltest.yml
Test #6 - README Nextflow minimum version badge matched config. Badge: 20.04.0, Config: 20.04.0
Test #6 - README had a bioconda badge
Test #8 - Conda environment name was correct (nf-core-eager-2.2.0dev)
Test #8 - Conda dependency had pinned version number: conda-forge::python=3.7.3
Test #8 - Conda dependency had pinned version number: conda-forge::markdown=3.2.2
Test #8 - Conda package is latest available: conda-forge::markdown=3.2.2
Test #8 - Conda dependency had pinned version number: conda-forge::pymdown-extensions=7.1
Test #8 - Conda dependency had pinned version number: conda-forge::pygments=2.6.1
Test #8 - Conda dependency had pinned version number: bioconda::rename=1.601
Test #8 - Conda package is latest available: bioconda::rename=1.601
Test #8 - Conda dependency had pinned version number: conda-forge::openjdk=8.0.144
Test #8 - Conda dependency had pinned version number: bioconda::fastqc=0.11.9
Test #8 - Conda package is latest available: bioconda::fastqc=0.11.9
Test #8 - Conda dependency had pinned version number: bioconda::adapterremoval=2.3.1
Test #8 - Conda package is latest available: bioconda::adapterremoval=2.3.1
Test #8 - Conda dependency had pinned version number: bioconda::adapterremovalfixprefix=0.0.5
Test #8 - Conda package is latest available: bioconda::adapterremovalfixprefix=0.0.5
Test #8 - Conda dependency had pinned version number: bioconda::bwa=0.7.17
Test #8 - Conda package is latest available: bioconda::bwa=0.7.17
Test #8 - Conda dependency had pinned version number: bioconda::picard=2.22.9
Test #8 - Conda dependency had pinned version number: bioconda::samtools=1.9
Test #8 - Conda dependency had pinned version number: bioconda::dedup=0.12.6
Test #8 - Conda package is latest available: bioconda::dedup=0.12.6
Test #8 - Conda dependency had pinned version number: bioconda::angsd=0.933
Test #8 - Conda package is latest available: bioconda::angsd=0.933
Test #8 - Conda dependency had pinned version number: bioconda::circularmapper=1.93.5
Test #8 - Conda package is latest available: bioconda::circularmapper=1.93.5
Test #8 - Conda dependency had pinned version number: bioconda::gatk4=4.1.7.0
Test #8 - Conda dependency had pinned version number: bioconda::qualimap=2.2.2d
Test #8 - Conda package is latest available: bioconda::qualimap=2.2.2d
Test #8 - Conda dependency had pinned version number: bioconda::vcf2genome=0.91
Test #8 - Conda package is latest available: bioconda::vcf2genome=0.91
Test #8 - Conda dependency had pinned version number: bioconda::damageprofiler=0.4.9
Test #8 - Conda dependency had pinned version number: bioconda::multiqc=1.9
Test #8 - Conda package is latest available: bioconda::multiqc=1.9
Test #8 - Conda dependency had pinned version number: bioconda::pmdtools=0.60
Test #8 - Conda package is latest available: bioconda::pmdtools=0.60
Test #8 - Conda dependency had pinned version number: bioconda::bedtools=2.29.2
Test #8 - Conda package is latest available: bioconda::bedtools=2.29.2
Test #8 - Conda dependency had pinned version number: conda-forge::libiconv=1.15
Test #8 - Conda dependency had pinned version number: conda-forge::pigz=2.3.4
Test #8 - Conda package is latest available: conda-forge::pigz=2.3.4
Test #8 - Conda dependency had pinned version number: bioconda::sequencetools=1.4.0.6
Test #8 - Conda package is latest available: bioconda::sequencetools=1.4.0.6
Test #8 - Conda dependency had pinned version number: bioconda::preseq=2.0.3
Test #8 - Conda package is latest available: bioconda::preseq=2.0.3
Test #8 - Conda dependency had pinned version number: bioconda::fastp=0.20.1
Test #8 - Conda package is latest available: bioconda::fastp=0.20.1
Test #8 - Conda dependency had pinned version number: bioconda::bamutil=1.0.14
Test #8 - Conda package is latest available: bioconda::bamutil=1.0.14
Test #8 - Conda dependency had pinned version number: bioconda::mtnucratio=0.7
Test #8 - Conda package is latest available: bioconda::mtnucratio=0.7
Test #8 - Conda dependency had pinned version number: pysam=0.15.4
Test #8 - Conda dependency had pinned version number: bioconda::kraken2=2.0.9beta
Test #8 - Conda package is latest available: bioconda::kraken2=2.0.9beta
Test #8 - Conda dependency had pinned version number: conda-forge::pandas=1.0.4
Test #8 - Conda dependency had pinned version number: bioconda::freebayes=1.3.2
Test #8 - Conda package is latest available: bioconda::freebayes=1.3.2
Test #8 - Conda dependency had pinned version number: bioconda::sexdeterrmine=1.1.2
Test #8 - Conda package is latest available: bioconda::sexdeterrmine=1.1.2
Test #8 - Conda dependency had pinned version number: bioconda::multivcfanalyzer=0.85.2
Test #8 - Conda package is latest available: bioconda::multivcfanalyzer=0.85.2
Test #8 - Conda dependency had pinned version number: bioconda::hops=0.34
Test #8 - Conda package is latest available: bioconda::hops=0.34
Test #8 - Conda dependency had pinned version number: conda-forge::biopython=1.76
Test #8 - Conda dependency had pinned version number: conda-forge::xopen=0.9.0
Test #8 - Conda package is latest available: conda-forge::xopen=0.9.0
Test #8 - Conda dependency had pinned version number: bioconda::bowtie2=2.4.1
Test #8 - Conda package is latest available: bioconda::bowtie2=2.4.1
Test #9 - Found all expected strings in Dockerfile file
Test #12 - Name adheres to nf-core convention
Test #13 - Did not find any cookiecutter template strings (137 files)
Test #14 - Schema lint passed
Test #14 - Schema title + description lint passed

Run details:

nf-core/tools version 1.10.2
Run at 2020-09-15 06:42:15

maxibor and others added 30 commits April 1, 2020 22:35

join bam and fastq channel

6828331

update changelog

cb04a6e

switch channels to tuples

d3f0450

fix more channels cardinality and dedup prefix

9cd4831

Adjusted fixes for AWS index handling

5dec901

Fix supplied indices and typo

a19e32b

Fix test

6b6d9ca

Zipped fasta it is

65048fc

Fix some more indices

8be5066

Fix path

fd43ba8

Fix strip_input

dea0244

Fix some more paths

ee4721f

Fix small malt issue

96fff7a

Merge branch 'dev' into fix-aws

95ccd01

Atttempt to fix last tmissing bits for index handlign

e1a5782

Merge branch 'fix-aws' of https://github.com/nf-core/eager into fix-aws

3a9d847

Some more fixes

e09082c

Prefix with def to fix

1e5c8a4

Make new dummy file replace Class() with instanceof and remove dummy NAs

fbb5309

One more

c20eb50

Stop file collisions

d13a078

Remove debugging code

1e4035b

Remove last code TODO after local testing

1096321

Merge branch 'fix-aws' into aws-syncing

bbb210f

Merge pull request #514 from nf-core/aws-syncing

f109a80

syncing

Make bwa input as path

fe4e8a3

Remove duplicate strip_fastq process

a477b0d

Fix inaccesible BAMs due to grouping of single elements when skipping…

ae33488

… everything

Remove debugging stuff

0330c6b

Add some more dumps

827d585

jfy133 and others added 26 commits August 25, 2020 13:02

Update benchmarking_pathogenscreening.config

5da8795

Update benchmarking_pathogenscreening.config

e8906c1

Move pathogen screening out of usage

03186ed

Linting

0aa1760

Merge branch 'dev' into docs-schema-update

d3c718f

More linting

5660c10

Merge branch 'docs-schema-update' of github.com:nf-core/eager into do…

8432209

…cs-schema-update

Linting again

c5363b3

Merge pull request #542 from nf-core/tsv-headername-validation

91518c9

Tsv headername validation

Merge pull request #538 from nf-core/docs-schema-update

baa0d60

Docs and schema update

merge upstream

1b2dfa8

multiprocessing, but not working

45d44eb

slower, but working solution

af024b2

merge from upstream

3d7ed0e

update changelog

c03a1a9

Move short time limits to test profiles, and bump base run times to 24h

8f175fd

Update changelog

102a62f

until_eof for unmapped reads

a40ae71

Merge pull request #544 from maxibor/dev

249d5f4

Add bam filtering on fragment length script

Replaced awk with python version of read filtering

8dd15e2

Merge pull request #550 from nf-core/dev

32dfeb0

Get final python script version

Merge pull request #549 from nf-core/new-bam-lengthfilter

3158d35

Replaced awk with python version of read filtering

Update base.config

8897be8

Update CHANGELOG.md

92e7b1a

Merge pull request #548 from nf-core/timelimit-mods

47c016b

Timelimit mods

Merge branch 'olgabot-patch-1' into olgabotpatch1-sync

2723a29

Update CHANGELOG.md

c2ad7a7

jfy133 merged commit a1bad01 into olgabot-patch-1 Sep 15, 2020

jfy133 deleted the olgabotpatch1-sync branch September 15, 2020 06:42

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Get latest dev version to check no flaky bam filtering#556

Get latest dev version to check no flaky bam filtering#556
jfy133 merged 156 commits intoolgabot-patch-1from
olgabotpatch1-sync

jfy133 commented Sep 15, 2020

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github-actions Bot commented Sep 15, 2020 •

edited

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❗ Test warnings:

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jfy133 commented Sep 15, 2020

nf-core/eager pull request

PR checklist

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github-actions Bot commented Sep 15, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core lint overall result: Passed ✅

❗ Test warnings:

✅ Tests passed:

Run details:

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github-actions Bot commented Sep 15, 2020 •

edited

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`nf-core lint` overall result: Passed ✅