Add dragmap aligner by edmundmiller · Pull Request #464 · nf-core/sarek

edmundmiller · 2021-12-07T15:15:52Z

Update docs
Update CI

If the code changes, look good those still need to be done.

github-actions · 2021-12-07T15:17:39Z

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

Posted for pipeline commit 2a677f9

+| ✅ 135 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
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: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

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nextflow_config - Config variable (correctly) not found: params.version
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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
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nextflow_config - Config dag.file ended with .svg
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files_unchanged - .gitattributes matches the template
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actions_ci - '.github/workflows/ci.yml' is triggered on expected events
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: 21.10.3, Config: 21.10.3
readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (252 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: local_modules.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

Run details

nf-core/tools version 2.2.dev0
Run at 2021-12-07 15:20:55

modules/nf-core/modules/dragmap/align/main.nf

maxulysse · 2021-12-07T15:24:00Z

subworkflows/local/prepare_genome.nf

+        } else if (params.aligner == "dragmap") {
+            DRAGMAP_HASHTABLE(fasta)
+            ch_bwa = DRAGMAP_HASHTABLE.out.hashmap
+            ch_versions = ch_versions.mix(DRAGMAP_HASHTABLE.out.versions)
        }


Should we have a placeholder in igenomes for this hashtable?

Even, I think it should be computed even when a bwa params is present

so maybe change bwa param to mapping_reference or something?

maxulysse · 2021-12-07T15:28:25Z

Can you had tests for it in tests/test_aligner.yml?

maxulysse · 2022-03-25T07:08:37Z

Looking super good.
I think we're still missing the actual align part, but I love this possibility

edmundmiller requested a review from maxulysse as a code owner December 7, 2021 15:15

edmundmiller force-pushed the dragmap branch from d3075f3 to 2a677f9 Compare December 7, 2021 15:19

FriederikeHanssen reviewed Dec 7, 2021

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modules/nf-core/modules/dragmap/align/main.nf Outdated Show resolved Hide resolved

maxulysse reviewed Dec 7, 2021

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This was referenced Dec 8, 2021

feat: update dragmap to follow new bwa/mem + bwamem2/mem logic nf-core/modules#1146

Merged

Remove local + update modules + nf-corize mapping subworkflow #466

Merged

edmundmiller force-pushed the dragmap branch from e4cfae1 to 9754661 Compare December 10, 2021 16:19

edmundmiller added 7 commits March 24, 2022 14:50

feat(prepare_genome): Add dragmap hashtable

57522f5

feat(mapping): Add dragmap align

9dae36c

chore(dragmap): Bump module

d3ea277

test(dragmap): Add basic test

e4e59df

fix(dragmap): Sort bam and update prefix

5ee771b

fix(dragmap): Add param to nextflow schema

301b69c

chore(dragmap): Bump modules

78791c0

edmundmiller force-pushed the dragmap branch from 8c6ed92 to 78791c0 Compare March 24, 2022 19:52

docs(dragmap): Add some notes

7a7509f

maxulysse mentioned this pull request Mar 25, 2022

Add dragmap #514

Merged

11 tasks

maxulysse merged commit 5247741 into nf-core:dev Mar 25, 2022

edmundmiller deleted the dragmap branch March 25, 2022 12:55

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Add dragmap aligner#464

Add dragmap aligner#464
maxulysse merged 8 commits intonf-core:devfrom
edmundmiller:dragmap

edmundmiller commented Dec 7, 2021 •

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nf-core lint overall result: Passed ✅ ⚠️

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edmundmiller commented Dec 7, 2021 •

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