Release 2.2.0 #176

GallVp · 2024-11-05T07:57:02Z

PR checklist

Version bumped to 2.2.0+dev

…er_min_bundle_size to 1000000

Reduced the GenomeTools stats figures to 300 DPI and set `synteny_mummer_min_bundle_size` is set to `1000000`

Added gfastats

Updated nf-core/template to 3.0.0

Fixed a bug where Gene score distribution graph did not appear correctly

Added explicit revision param to docs

Added parameter `hic_samtools_ext_args`

Added the HiC QC report to the final report

Added the fastp log to the final report

Added OrthoFinder and updated the tube map

… preferences related errors

Updated PFR's Kraken 2 and started using _JAVA_OPTIONS in RUNASSEMBLYVISUALIZER

github-actions · 2024-11-05T07:58:55Z

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

Posted for pipeline commit b4ced2a

+| ✅ 166 tests passed       |+
#| ❔  33 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

schema_lint - Schema $id should be https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/nextflow_schema.json
Found https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-assemblyqc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: validation.help.beforeText
nextflow_config - Config variable ignored: validation.help.afterText
nextflow_config - Config variable ignored: validation.summary.beforeText
nextflow_config - Config variable ignored: validation.summary.afterText
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File does not exist: assets/nf-core-assemblyqc_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/assemblyqc/assemblyqc/.github/workflows/awstest.yml
template_strings - template_strings
multiqc_config - multiqc_config
included_configs - included_configs

✅ 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: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.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/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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: main.nf
files_exist - File found: conf/base.config
files_exist - File found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-assemblyqc_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowAssemblyqc.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: 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: validation.help.enabled
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: validation.help.command
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 variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 2.2.0
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.check_sequence_duplicates= true
nextflow_config - Config default value correct: params.assemblathon_stats_n_limit= 100
nextflow_config - Config default value correct: params.gfastats_skip= true
nextflow_config - Config default value correct: params.ncbi_fcs_adaptor_skip= true
nextflow_config - Config default value correct: params.ncbi_fcs_gx_skip= true
nextflow_config - Config default value correct: params.contamination_stops_pipeline= true
nextflow_config - Config default value correct: params.tidk_skip= true
nextflow_config - Config default value correct: params.tidk_filter_size_bp= 1000000
nextflow_config - Config default value correct: params.busco_skip= true
nextflow_config - Config default value correct: params.lai_skip= true
nextflow_config - Config default value correct: params.kraken2_skip= true
nextflow_config - Config default value correct: params.hic_fastp_ext_args= --qualified_quality_phred 20 --length_required 50
nextflow_config - Config default value correct: params.hic_samtools_ext_args= -F 3852
nextflow_config - Config default value correct: params.merqury_skip= true
nextflow_config - Config default value correct: params.merqury_kmer_length= 21
nextflow_config - Config default value correct: params.synteny_skip= true
nextflow_config - Config default value correct: params.synteny_mummer_skip= true
nextflow_config - Config default value correct: params.synteny_plotsr_skip= true
nextflow_config - Config default value correct: params.synteny_between_input_assemblies= true
nextflow_config - Config default value correct: params.synteny_mummer_plot_type= both
nextflow_config - Config default value correct: params.synteny_mummer_max_gap= 1000000
nextflow_config - Config default value correct: params.synteny_mummer_min_bundle_size= 1000000
nextflow_config - Config default value correct: params.synteny_color_by_contig= true
nextflow_config - Config default value correct: params.synteny_plotsr_seq_label= Chr
nextflow_config - Config default value correct: params.orthofinder_skip= true
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.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
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - NCBI_FCS_GX_SCREEN_SAMPLES found in conf/base.config and Nextflow scripts.
base_config - KRAKEN2 found in conf/base.config and Nextflow scripts.
base_config - BWA_MEM found in conf/base.config and Nextflow scripts.
base_config - SAMBLASTER found in conf/base.config and Nextflow scripts.
base_config - DNADIFF found in conf/base.config and Nextflow scripts.
base_config - MERQURY_HAPMERS found in conf/base.config and Nextflow scripts.
base_config - CREATEREPORT found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.0.2
Run at 2024-11-05 08:32:25

Excluded included_configs from linting

GallVp added 30 commits September 30, 2024 18:33

Version bumped to 2.2.0+dev

fdaa2f9

Merge pull request #143 from Plant-Food-Research-Open/bump/version

2c5bbc4

Version bumped to 2.2.0+dev

Reduced the GenomeTools stats figures to 300 DPI and set synteny_mumm…

bbb0177

…er_min_bundle_size to 1000000

Updated params

bf337ba

Merge pull request #144 from Plant-Food-Research-Open/optimise/report

89b9e5a

Reduced the GenomeTools stats figures to 300 DPI and set `synteny_mummer_min_bundle_size` is set to `1000000`

Added gfastats

98ff46c

Updated changelog

fc0f989

Added description for gfastats_skip

fba2ea0

Merge pull request #145 from Plant-Food-Research-Open/add/gfastats

dd7bd92

Added gfastats

Template update for nf-core/tools version 3.0.0

87f4f4a

Merge branch 'TEMPLATE' into update/template

929b11f

Updated nf-core/template to 3.0.0

9fc7989

Fixed schema issues

c81f941

Removed unnecessary params

2dfe368

Removed max resource params

8817696

Fixed linting issues

30b8e2e

Migrated to [email protected]

1404b29

Fixed test_full issues

7afc159

Removed validate_params

67db39d

Updated params

9096eb8

Updated CI

eeae0f2

Fixed CI and linting issues

3946d57

Linting fix

717fbf2

Fixed nf-test

559266e

Merge pull request #150 from Plant-Food-Research-Open/update/template

97df745

Updated nf-core/template to 3.0.0

Fixed a bug where Gene score distribution graph did not appear correctly

eeaaf3f

Fixed ci and params

6a77321

Merge pull request #148 from Plant-Food-Research-Open/fix/gtplot

6eef70b

Fixed a bug where Gene score distribution graph did not appear correctly

Template update for nf-core/tools version 3.0.1

966c6b2

Updated nf-core/template to 3.0.1

8fd1b9e

GallVp added 26 commits October 25, 2024 15:33

Merge pull request #164 from Plant-Food-Research-Open/docs/rev

abd4695

Added explicit revision param to docs

Added parameter hic_samtools_ext_args

c1f83cc

Merge pull request #165 from Plant-Food-Research-Open/hic/filter

26025a4

Added parameter `hic_samtools_ext_args`

Added the HiC QC report to the final report

5c769fa

Updated outputs

5f373d6

Merge pull request #171 from Plant-Food-Research-Open/report/hicqc

14ca56e

Added the HiC QC report to the final report

Added the fastp log to the final report

d4624de

Merge pull request #172 from Plant-Food-Research-Open/report/fastp

d410971

Added the fastp log to the final report

Added orthofinder

2e8844d

Update flowchart

3c2c872

Update flowchart

936bb2f

Updated docs

fb206c4

Fixed a couple of typos

4f8222e

Merge pull request #174 from Plant-Food-Research-Open/add/orthofinder

10a4bd7

Added OrthoFinder and updated the tube map

Moved around test_full options

abd8f51

Updated pfr params

c7998d6

Updated pfr_assembly launch script

8fcc5ce

Version bump and a couple of minor fixes

cf11c1b

Updated PFR's Kraken 2 database to k2_pluspfp_20240904

af5c449

Increased memory requirement for Kraken 2 to 256.GB

e140509

Updated docs and removed resource limits from test_full

d98384a

Updated synteny_mummer_min_bundle_size for pfr/params

0da7cea

Now using _JAVA_OPTIONS in module RUNASSEMBLYVISUALIZER to avoid user…

e6b968f

… preferences related errors

Now added user.home property to JAVA_OPTIONS

0f9a4ee

Fixed version mismatches

ddc9aae

Merge pull request #175 from Plant-Food-Research-Open/release/test

8a7d09c

Updated PFR's Kraken 2 and started using _JAVA_OPTIONS in RUNASSEMBLYVISUALIZER

GallVp added 2 commits November 5, 2024 21:18

Excluded included_configs from linting

ab0f094

Merge pull request #177 from Plant-Food-Research-Open/fix/linting

b4ced2a

Excluded included_configs from linting

GallVp merged commit 0141925 into main Nov 5, 2024
75 checks passed

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Release 2.2.0 #176

Release 2.2.0 #176

GallVp commented Nov 5, 2024

github-actions bot commented Nov 5, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Release 2.2.0 #176

Release 2.2.0 #176

Conversation

GallVp commented Nov 5, 2024

PR checklist

github-actions bot commented Nov 5, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Nov 5, 2024 •

edited

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