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Trio #55

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yumisims
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@yumisims yumisims commented Sep 23, 2024 •
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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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Sep 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 36730fc

+| ✅ 130 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_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
  • 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 ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomeassembly/genomeassembly/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-09-23 21:52:02

@ksenia-krasheninnikova
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Hi @yumisims
Looks good to me in general, thanks for your work! What has to be changed - we don't have to run purge_dups when hifiasm is run in the trio mode. The logic is similar to the the hap1/hap2 assembly - each of the two hifiasm trio-phased files is to be scaffolded up directly:

genomeassembly/workflows/genomeassembly.nf

Lines 388 to 430 in 36730fc

if ( hifiasm_hic_on ) {
//
// SUBWORKFLOW: MAP HIC DATA TO THE HAP1 CONTIGS
//
HIC_MAPPING_HAP1 ( RAW_ASSEMBLY.out.hap1_hic_contigs, crams_ch, hic_aligner_ch, 'hap1' )
ch_versions = ch_versions.mix(HIC_MAPPING_HAP1.out.versions)
//
// SUBWORKFLOW: SCAFFOLD HAP1
//
SCAFFOLDING_HAP1( HIC_MAPPING_HAP1.out.bed, RAW_ASSEMBLY.out.hap1_hic_contigs, cool_bin, 'hap1' )
ch_versions = ch_versions.mix(SCAFFOLDING_HAP1.out.versions)
//
// SUBWORKFLOW: MAP HIC DATA TO THE HAP2 CONTIGS
//
HIC_MAPPING_HAP2 ( RAW_ASSEMBLY.out.hap2_hic_contigs, crams_ch, hic_aligner_ch, 'hap2' )
ch_versions = ch_versions.mix(HIC_MAPPING_HAP2.out.versions)
//
// SUBWORKFLOW: SCAFFOLD HAP2
//
SCAFFOLDING_HAP2( HIC_MAPPING_HAP2.out.bed, RAW_ASSEMBLY.out.hap2_hic_contigs, cool_bin, 'hap2' )
ch_versions = ch_versions.mix(SCAFFOLDING_HAP2.out.versions)
//
// LOGIC: CREATE A CHANNEL FOR THE FULL HAP1/HAP2 ASSEMBLY
//
SCAFFOLDING_HAP1.out.fasta.combine(SCAFFOLDING_HAP2.out.fasta)
.map{meta_s, fasta_s, meta_h, fasta_h -> [ [id:meta_h.id], fasta_s, fasta_h ]}
.set{ stats_haps_input_ch }
//
// SUBWORKFLOW: CALCULATE ASSEMBLY STATISTICS FOR HAP1/HAP2 ASSEMBLY
//
GENOME_STATISTICS_SCAFFOLDS_HAPS( stats_haps_input_ch,
PREPARE_INPUT.out.busco,
GENOMESCOPE_MODEL.out.hist,
GENOMESCOPE_MODEL.out.ktab,
[],
[],
set_busco_alts
)

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@ksenia-krasheninnikova ksenia-krasheninnikova Awaiting requested review from ksenia-krasheninnikova

@gq1 gq1 Awaiting requested review from gq1

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@yumisims @ksenia-krasheninnikova