New version 1.3.0 by nservant · Pull Request #101 · nf-core/hic

nservant · 2021-05-13T14:09:11Z

Release new nf-core-hic version

nf-core template merge v1.11

Update issue templates

Important! Template update for nf-core/tools v1.12

[MODIF] update input parameters

maxulysse · 2021-05-13T14:16:03Z

 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile
-RUN touch .Renviron
+RUN touch .Renviron


I believe this is not in the TEMPLATE anymore

cf https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/Dockerfile

I prefer to keep it so far, to avoid any issue with R local library. Is it ok ?

maxulysse

LGTM,
If you fix the typo, you'll need to add the corresponding files to .nf-core-lint.yml:
cf https://github.com/nf-core/eager/blob/master/.nf-core-lint.yml

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

nservant · 2021-05-13T16:22:17Z

Hi @maxulysse . Thanks for the review !
Should I add a .nf-core-lint.yml file ? Thanks

nservant · 2021-05-13T16:23:41Z

ah yes. got it. I'll add the file

add .nf-core-lint.yml

mashehu

LGTM, just some smaller things you need to fix/look at, before I'll give the final 👍

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Add patern for all comma separated string options

nservant · 2021-05-24T16:45:26Z

Hi @mashehu,
I think I fixed all your comments. Could you please validate the PR.
Many thanks for your help and for the review !
N

github-actions · 2021-05-24T19:00:55Z

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

Posted for pipeline commit 1638467

+| ✅ 218 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  19 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.3.0'
conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.6, 3.9.4 available
conda_env_yaml - Conda dep outdated: pip=20.0.1, 21.1.2 available
conda_env_yaml - Conda dep outdated: conda-forge::tbb=2020.2=hc9558a2_0, 2021.2.0 available
conda_env_yaml - Conda dep outdated: conda-forge::scipy=1.4.1, 1.6.3 available
conda_env_yaml - Conda dep outdated: conda-forge::numpy=1.18.1, 1.20.3 available
conda_env_yaml - Conda dep outdated: bioconda::iced=0.5.6, 0.5.8 available
conda_env_yaml - Conda dep outdated: bioconda::bx-python=0.8.8, 0.8.11 available
conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.4, 0.16.0 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.2 available
conda_env_yaml - Conda dep outdated: bioconda::cooler=0.8.6, 0.8.11 available
conda_env_yaml - Conda dep outdated: bioconda::bowtie2=2.3.5, 2.4.3 available
conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.8, 1.10.1 available
conda_env_yaml - Conda dep outdated: bioconda::hicexplorer=3.4.3, 3.6 available
conda_env_yaml - Conda dep outdated: bioconda::bioconductor-hitc=1.32.0, 1.34.0 available
conda_env_yaml - Conda dep outdated: bioconda::ucsc-bedgraphtobigwig=357, 377 available
conda_env_yaml - Conda dep outdated: conda-forge::cython=0.29.19, 0.29.23 available
conda_env_yaml - PyPI package is not latest available: 0.8.30, 0.9.18 available

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: CHANGELOG.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.md
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File found: .github/markdownlint.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-hic_logo.png
files_exist - File found: bin/markdown_to_html.py
files_exist - File found: docs/images/nf-core-hic_logo.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: main.nf
files_exist - File found: environment.yml
files_exist - File found: Dockerfile
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 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: .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 found: process.container
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 process.container looks correct: nfcore/hic:1.3.0
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
params_used - Config variable found in main.nf: params.genome
params_used - Config variable found in main.nf: params.input
params_used - Config variable found in main.nf: params.input_paths
params_used - Config variable found in main.nf: params.outdir
params_used - Config variable found in main.nf: params.chromosome_size
params_used - Config variable found in main.nf: params.restriction_fragments
params_used - Config variable found in main.nf: params.save_reference
params_used - Config variable found in main.nf: params.split_fastq
params_used - Config variable found in main.nf: params.fastq_chunks_size
params_used - Config variable found in main.nf: params.save_interaction_bam
params_used - Config variable found in main.nf: params.save_aligned_intermediates
params_used - Config variable found in main.nf: params.bwt2_opts_end2end
params_used - Config variable found in main.nf: params.bwt2_opts_trimmed
params_used - Config variable found in main.nf: params.keep_dups
params_used - Config variable found in main.nf: params.keep_multi
params_used - Config variable found in main.nf: params.min_mapq
params_used - Config variable found in main.nf: params.digestion
params_used - Config variable found in main.nf: params.min_restriction_fragment_size
params_used - Config variable found in main.nf: params.max_restriction_fragment_size
params_used - Config variable found in main.nf: params.min_insert_size
params_used - Config variable found in main.nf: params.max_insert_size
params_used - Config variable found in main.nf: params.save_nonvalid_pairs
params_used - Config variable found in main.nf: params.dnase
params_used - Config variable found in main.nf: params.min_cis_dist
params_used - Config variable found in main.nf: params.bin_size
params_used - Config variable found in main.nf: params.res_zoomify
params_used - Config variable found in main.nf: params.hicpro_maps
params_used - Config variable found in main.nf: params.ice_max_iter
params_used - Config variable found in main.nf: params.ice_filter_low_count_perc
params_used - Config variable found in main.nf: params.ice_filter_high_count_perc
params_used - Config variable found in main.nf: params.ice_eps
params_used - Config variable found in main.nf: params.res_dist_decay
params_used - Config variable found in main.nf: params.tads_caller
params_used - Config variable found in main.nf: params.res_tads
params_used - Config variable found in main.nf: params.res_compartments
params_used - Config variable found in main.nf: params.skip_maps
params_used - Config variable found in main.nf: params.skip_balancing
params_used - Config variable found in main.nf: params.skip_mcool
params_used - Config variable found in main.nf: params.skip_dist_decay
params_used - Config variable found in main.nf: params.skip_compartments
params_used - Config variable found in main.nf: params.skip_tads
params_used - Config variable found in main.nf: params.skip_multiqc
params_used - Config variable found in main.nf: params.publish_dir_mode
params_used - Config variable found in main.nf: params.multiqc_config
params_used - Config variable found in main.nf: params.email
params_used - Config variable found in main.nf: params.email_on_fail
params_used - Config variable found in main.nf: params.max_multiqc_email_size
params_used - Config variable found in main.nf: params.plaintext_email
params_used - Config variable found in main.nf: params.monochrome_logs
params_used - Config variable found in main.nf: params.help
params_used - Config variable found in main.nf: params.tracedir
params_used - Config variable found in main.nf: params.hostnames
params_used - Config variable found in main.nf: params.config_profile_description
params_used - Config variable found in main.nf: params.config_profile_contact
params_used - Config variable found in main.nf: params.config_profile_url
params_used - Config variable found in main.nf: params.validate_params
params_used - Config variable found in main.nf: params.max_memory
params_used - Config variable found in main.nf: params.max_cpus
params_used - Config variable found in main.nf: params.max_time
params_used - Config variable found in main.nf: params.restriction_site
params_used - Config variable found in main.nf: params.ligation_site
params_used - Config variable found in main.nf: params.bwt2_index
params_used - Config variable found in main.nf: params.fasta
files_unchanged - .gitattributes 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/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
files_unchanged - .github/markdownlint.yml 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-hic_logo.png matches the template
files_unchanged - bin/markdown_to_html.py matches the template
files_unchanged - docs/images/nf-core-hic_logo.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 - .gitignore matches the template
files_unchanged - .github/workflows/push_dockerhub_dev.yml matches the template
files_unchanged - .github/workflows/push_dockerhub_release.yml matches the template
files_unchanged - assets/multiqc_config.yaml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - CI is building the correct docker image: docker build --no-cache . -t nfcore/hic:1.3.0
actions_ci - CI is pulling the correct docker image: docker pull nfcore/hic:dev
actions_ci - CI is tagging docker image correctly: docker tag nfcore/hic:dev nfcore/hic:1.3.0
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: 20.04.0, Config: 20.04.0
readme - README had a bioconda badge
conda_env_yaml - Conda environment name was correct (nf-core-hic-1.3.0)
conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.6
conda_env_yaml - Conda dep had pinned version number: pip=20.0.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::tbb=2020.2=hc9558a2_0
conda_env_yaml - Conda dep had pinned version number: conda-forge::scipy=1.4.1
conda_env_yaml - Conda dep had pinned version number: conda-forge::numpy=1.18.1
conda_env_yaml - Conda dep had pinned version number: bioconda::iced=0.5.6
conda_env_yaml - Conda dep had pinned version number: bioconda::bx-python=0.8.8
conda_env_yaml - Conda dep had pinned version number: bioconda::pysam=0.15.4
conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=7.1
conda_env_yaml - Conda dep had pinned version number: bioconda::cooler=0.8.6
conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.3.5
conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.9
conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.8
conda_env_yaml - Conda dep had pinned version number: bioconda::hicexplorer=3.4.3
conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-hitc=1.32.0
conda_env_yaml - Conda dep had pinned version number: conda-forge::r-optparse=1.6.6
conda_env_yaml - Conda package is the latest available: conda-forge::r-optparse=1.6.6
conda_env_yaml - Conda dep had pinned version number: bioconda::ucsc-bedgraphtobigwig=357
conda_env_yaml - Conda dep had pinned version number: conda-forge::cython=0.29.19
conda_env_yaml - Pip dependency had pinned version number: cooltools==0.4.0
conda_env_yaml - PyPI package is latest available: 0.4.0
conda_env_yaml - Pip dependency had pinned version number: fanc==0.8.30
conda_dockerfile - Found all expected strings in Dockerfile file
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (57 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: ci.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.14
Run at 2021-05-24 16:58:25

nf-core-bot and others added 30 commits October 27, 2020 09:25

Template update for nf-core/tools version 1.11

1ee1d69

Update issue templates

489e6c0

Apply suggestions from code review

a7584ae

Merge upstream 'TEMPLATE' from nf-core v1.11

586bfc3

Add back pipeline logo images which were deleted in the template merge

b93833f

nf-core bump versions to pipeline version 1.3dev

3634558

Fix markdownlint errors

2fbc38f

Change version to 1.3.0dev

479a390

Bring standard summary log messages in line with template

a67507a

Changelog

3abd228

Merge pull request #79 from ewels/nf-core-template-merge-1.11

28aeafa

nf-core template merge v1.11

Merge remote-tracking branch 'origin/dev' into updated-issue-templates

053c1e9

Merge pull request #78 from nf-core/updated-issue-templates

1df8649

Update issue templates

Template update for nf-core/tools version 1.12

acee335

Merge branch 'dev' into TEMPLATE

5d1f226

Merge pull request #82 from nf-core/TEMPLATE

982b70b

Important! Template update for nf-core/tools v1.12

[MODIF] update input parameters

ac3967c

remove single_end from config

8110985

[BUG] fix bug in --bin-size parameter #85

861805c

[MODIF] new digestion parameter

c9223c8

[DOC] update usage.md

47e9583

[MODIF] fix bug in software version

e7852f9

[MODIF] fix input extension errors

44a7178

[MODIF] update in mqc report

10e9c12

[MODIF] update test profile

3cf7422

[MODIF] update test profile

0ace3e0

Merge pull request #84 from nservant/dev

9621345

[MODIF] update input parameters

update changelog

66adbd0

Merge branch 'dev' of https://github.com/nf-core/nf-core-hic into dev

a4f91d7

[MODIF] add tads calling

e51d04f

maxulysse reviewed May 13, 2021

View reviewed changes

nservant and others added 3 commits May 13, 2021 18:11

Update .github/PULL_REQUEST_TEMPLATE.md

893fd30

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

Update .github/ISSUE_TEMPLATE/bug_report.md

ec18e14

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

Update Dockerfile

b426a26

nservant added 4 commits May 13, 2021 18:26

Add nf-core lint file

96cb096

Add nf-core lint file

7c54e7d

Add nf-core lint file

aef29f5

Merge pull request #102 from nservant/dev

e8ad1e2

add .nf-core-lint.yml

maxulysse approved these changes May 20, 2021

View reviewed changes

mashehu reviewed May 20, 2021

View reviewed changes

nservant and others added 7 commits May 21, 2021 13:08

Update CHANGELOG.md

f668816

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update main.nf

cadac37

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update main.nf

b2bf20a

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update docs/usage.md

3ff6af5

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update docs/usage.md

3ed7b6d

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update main.nf

40b544c

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update main.nf

f34f7a0

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

nservant mentioned this pull request May 21, 2021

Usage page #103

Closed

nservant added 3 commits May 21, 2021 19:23

Update usage.md

8c37878

Update CHANGELOG.md

f9deac7

Update nextflow_schema.json

7612617

Add patern for all comma separated string options

nservant added 2 commits May 24, 2021 18:51

Update nextflow_schema.json

4c1b3c2

Update nextflow_schema.json

1638467

mashehu approved these changes May 24, 2021

View reviewed changes

nservant merged commit ac74763 into master May 24, 2021

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nservant commented May 24, 2021

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github-actions Bot commented May 24, 2021

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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