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bwa-mem / pairtools #174

Merged
merged 34 commits into from
Mar 6, 2024
Merged

bwa-mem / pairtools #174

merged 34 commits into from
Mar 6, 2024

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nservant
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@nservant nservant commented Jun 26, 2023 •
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Initial merge

The PR contains the first version of the bwa-mem/pairtools sub-workflow.
Additional validations are on-going

nservant added 27 commits April 26, 2023 14:45
@nservant
[MODIF] add arimaV2 restriction motifs
7764e12
@nservant
Merge branch 'dev' of https://github.com/nf-core/hic into dev
1ed8c3d
@nservant
[MODIF] add pairtools nf-core#162
8d40b36
@nservant
[MODIF] add pairtools nf-core#162
a4a546e
@nservant
[MODIF] first test
e47c088
@nservant
[MODIF] fix insulation has default tads caller
3ba065a
@nservant
[MODIF] compare pairtools and hicpro
407c063
@nservant
[schema] update default
0abac64
@nservant
[MODIF] update README
7bfbd8c
@nservant
[MODIF] update README
722a43c
@nservant
[MODIF] update bowtie2 module
c257b67
@nservant
[MODIF] use groupKey
76aa380
@nservant
[MODIF] pairtools fix
d704b62
@nservant
[MODIF] fix typo
2857c66
@nservant
[MODIF] bug in modules
14d2113
@nservant
[MODIF] add samtools sort
07e19f4
@nservant
[MODIF] update docs
05a06c1
@nservant
[MODIF] update docs
48534b1
@nservant
[MODIF] update docs
edeb250
@nservant
[MODIF] update docs
10df354
@nservant
[MODIF] update docs
a6c25ce
@nservant
[MODIF] update sort pairtool
e3e3493
@nservant
[MODIF] bug in microC
972a593
@nservant
[MODIF] update in mapq filter for pairtools
fbb7680
@nservant
[MODIF] fix pairtools subwkflow
66d4791
@nservant
[MODIF] typo
2a5d08c
@nservant
Merge branch 'dev' into dev
38f1ee9
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github-actions bot commented Jan 26, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 4f2d24a

+| ✅ 162 tests passed       |+
-| ❌  26 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • nextflow_config - Config default value incorrect: params.bwt2_opts_end2end is set as '--very-sensitive --end-to-end --reorder' in nextflow_schema.json but is --very-sensitive --end-to-end --reorder in nextflow.config.
  • nextflow_config - Config default value incorrect: params.bwt2_opts_trimmed is set as '--very-sensitive --end-to-end --reorder' in nextflow_schema.json but is --very-sensitive --end-to-end --reorder in nextflow.config.
  • nextflow_config - Config default value incorrect: params.bwa_opts is set as '-5SP -T0' in nextflow_schema.json but is -5SP -T0 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.bin_size is set as 1000000,500000 in nextflow_schema.json but is 1000000 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.res_zoomify is set as 5000 in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.res_dist_decay is set as 1000000 in nextflow_schema.json but is 250000 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.res_tads is set as 40000,20000 in nextflow_schema.json but is 40000 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.tracedir is set as ${params.outdir}/pipeline_info in nextflow_schema.json but is ./results/pipeline_info in nextflow.config.
  • files_unchanged - CODE_OF_CONDUCT.md does not match the template
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-hic_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-hic_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-hic_logo_dark.png does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • files_unchanged - pyproject.toml does not match the template
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/hic/tree/dev" target="_blank">nf-core/hic</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/hic/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/hic" target="_blank">documentation</a>.

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-15 07:14:22

@nservant nservant requested a review from maxulysse January 26, 2024 15:35
@nservant nservant added the enhancement New feature or request label Jan 26, 2024
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Would be great to merge this version before morging the code template to avoid too many issues.
Of note, this is not yet a pre-release ... a few more tests/devs are ongoing

@nservant nservant mentioned this pull request Jan 26, 2024
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@nf-core-bot fix linting

maxulysse
maxulysse approved these changes Feb 15, 2024
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LGTM

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I'd reckon merging TEMPLATE would be good too, cf #191

@nservant nservant merged commit a83615a into nf-core:dev Mar 6, 2024
4 of 6 checks passed
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github-actions bot commented Mar 6, 2024

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@edmundmiller edmundmiller added this to the version-2.2.0 milestone Mar 6, 2024
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@maxulysse maxulysse maxulysse approved these changes

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