feat(modules): update all modules #1457

maxulysse · 2024-04-05T11:45:34Z

PR checklist

github-actions · 2024-04-05T11:49:05Z

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

Posted for pipeline commit 2a3e955

+| ✅ 181 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/NfcoreTemplate.groovy
files_exist - File is ignored: lib/WorkflowSarek.groovy
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
template_strings - template_strings

✅ 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: 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-sarek_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
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-sarek_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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.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 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: 3.5dev
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.step= mapping
nextflow_config - Config default value correct: params.split_fastq= 50000000
nextflow_config - Config default value correct: params.nucleotides_per_second= 200000
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.trim_nextseq= 0
nextflow_config - Config default value correct: params.group_by_umi_strategy= Adjacency
nextflow_config - Config default value correct: params.aligner= bwa-mem
nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
nextflow_config - Config default value correct: params.ascat_min_counts= 10
nextflow_config - Config default value correct: params.ascat_min_map_qual= 35
nextflow_config - Config default value correct: params.cf_coeff= 0.05
nextflow_config - Config default value correct: params.cf_contamination= 0
nextflow_config - Config default value correct: params.cf_minqual= 0
nextflow_config - Config default value correct: params.cf_mincov= 0
nextflow_config - Config default value correct: params.cf_ploidy= 2
nextflow_config - Config default value correct: params.sentieon_haplotyper_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_pcr_indel_model= CONSERVATIVE
nextflow_config - Config default value correct: params.dbnsfp_fields= rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
nextflow_config - Config default value correct: params.vep_custom_args= --everything --filter_common --per_gene --total_length --offline --format vcf
nextflow_config - Config default value correct: params.vep_version= 110.0-0
nextflow_config - Config default value correct: params.vep_out_format= vcf
nextflow_config - Config default value correct: params.genome= GATK.GRCh38
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.vep_cache= s3://annotation-cache/vep_cache/
nextflow_config - Config default value correct: params.snpeff_cache= s3://annotation-cache/snpeff_cache/
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.test_data_base= https://raw.githubusercontent.com/nf-core/test-datasets/sarek3
nextflow_config - Config default value correct: params.seq_platform= ILLUMINA
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
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/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 - docs/README.md matches the template
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ncbench.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: cloudtest.yml
actions_schema_validation - Workflow validation passed: branch.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' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
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'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-04-10 07:47:34

subworkflows/local/cram_qc_mosdepth_samtools/main.nf

SPPearce · 2024-04-09T12:54:32Z

subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf

-    BWAMEM1_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem
-    BWAMEM2_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem2
-    DRAGMAP_ALIGN(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is dragmap
+    BWAMEM1_MEM(reads, index, [[id:'no_fasta'], []], sort) // If aligner is bwa-mem


Why do these not want the fasta files?

because we're not doing cram at that point yet

Yes, but the fasta channel is already there, so why not just use it?

useless if we don't create CRAM, and it would be a waste to store if not used

But it'll only be passed as a symlink into the folder. Just don't see the reason to create a dummy variable for something that is already defined.

I like the usage of [[id:'no_fasta'], []] as input here instead of the fasta, as it also makes it clear to me that BWAMEM1_MEM doesn't use the fasta.

subworkflows/local/prepare_genome/main.nf

workflows/sarek/main.nf

modules/nf-core/samtools/convert/main.nf

conf/modules/annotate.config

Co-authored-by: Simon Pearce <[email protected]>

SPPearce

Looks good to me.

adamrtalbot

A lot of hidden diffs which I didn't check. Not sure what the changes are in the module configs?

main.nf

SPPearce

Still not sure on the logic behind passing a dummy fasta rather than the actual fasta, but not going to get hung up about it.

maxulysse added 2 commits April 5, 2024 13:45

feat(modules): update all modules

f13c4a9

feat(modules): patch bcftools/annotate

78a1fcd

maxulysse added 27 commits April 5, 2024 13:52

proper usage of new bwamem module

b625cde

update CHANGELOG

b3b8cd1

fix dragmap_align usage

b638419

properly patch controlfreec/assesssignificance

4241cfe

patch dragmap/hashtable

3b2ba8a

update CHANGELOG

01c947b

fix freebayes usage

9368503

update CHANGELOG

659155d

fix samtools/convert usage

0cecdd0

update snapshots

0f5c9ad

update ci skip list

681026a

update diff for controlfreec/assesssignificance

995ee59

Merge branch 'dev' into updates

8b8e5bb

update dragmap/hashtable

a8e7467

update samtools/faidx tests

0426f9a

freebayes: fix channels

8ae6604

Merge branch 'dev' into updates

6185e61

exlude some tags from CI

7dfd512

fasta and dependant indexes have meta maps

50c5a21

fasta and dependant indexes have meta maps

1a75992

fasta and dependant indexes have meta maps

3732e5d

simplify channels' meta

7aa3f95

update channels' meta

fd861c7

update channels' meta

1be890f

update channels' meta

b717523

fix channels' meta for preprocessing

8d4c903

more exclude tags

c507339

maxulysse added 2 commits April 9, 2024 11:11

fix md5sum

ecbfbf4

fix channels cardinallity

c21d08b

maxulysse marked this pull request as ready for review April 9, 2024 09:35

maxulysse requested a review from FriederikeHanssen as a code owner April 9, 2024 09:35

maxulysse added 10 commits April 9, 2024 11:39

update mutect2 tests

402fc57

update tags to exclude

94545f3

fix channels cardinality

fda1f97

fix channels cardinality

d3ccfe9

fix channel cardinality

fc48b49

create summary in config

676e719

fix md5sum

8ec2fcf

fix summary.html

8823d7f

fix md5sum

cccbbd9

update md5sum

7f746d3

SPPearce reviewed Apr 9, 2024

View reviewed changes

maxulysse and others added 3 commits April 9, 2024 15:12

fix channel cardinality

fcbb9c8

code polish

76d569c

Update subworkflows/local/cram_qc_mosdepth_samtools/main.nf

b9cfd1b

Co-authored-by: Simon Pearce <[email protected]>

SPPearce previously approved these changes Apr 9, 2024

View reviewed changes

maxulysse added 2 commits April 9, 2024 18:09

code polish

c2d1fd4

collect

0b3d82d

maxulysse dismissed SPPearce’s stale review via 0b3d82d April 9, 2024 16:09

adamrtalbot previously approved these changes Apr 9, 2024

View reviewed changes

main.nf Show resolved Hide resolved

update md5sum

2a3e955

maxulysse dismissed adamrtalbot’s stale review via 2a3e955 April 10, 2024 07:45

maxulysse requested review from adamrtalbot and SPPearce April 10, 2024 07:48

SPPearce approved these changes Apr 10, 2024

View reviewed changes

adamrtalbot approved these changes Apr 10, 2024

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maxulysse merged commit e32d0df into nf-core:dev Apr 10, 2024
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feat(modules): update all modules #1457

feat(modules): update all modules #1457

maxulysse commented Apr 5, 2024

github-actions bot commented Apr 5, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

SPPearce Apr 9, 2024

maxulysse Apr 9, 2024

SPPearce Apr 9, 2024

maxulysse Apr 9, 2024

SPPearce Apr 9, 2024

asp8200 Apr 10, 2024 •

edited

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feat(modules): update all modules #1457

feat(modules): update all modules #1457

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maxulysse commented Apr 5, 2024

PR checklist

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

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

SPPearce Apr 9, 2024

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github-actions bot commented Apr 5, 2024 •

edited

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

asp8200 Apr 10, 2024 •

edited

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