Add dragmap aligner #464

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 |!

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merge_markers - No merge markers found in pipeline files
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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modules/nf-core/modules/dragmap/align/main.nf Outdated Show resolved Hide resolved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

edmundmiller commented Dec 7, 2021 •

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github-actions bot commented Dec 7, 2021 •

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❗ Test warnings:

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✅ Tests passed:

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maxulysse Dec 7, 2021

maxulysse Dec 7, 2021

FriederikeHanssen Dec 8, 2021

maxulysse commented Dec 7, 2021

maxulysse commented Mar 25, 2022

Add dragmap aligner #464

Add dragmap aligner #464

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edmundmiller commented Dec 7, 2021 • edited Loading

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse Dec 7, 2021

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maxulysse commented Mar 25, 2022

edmundmiller commented Dec 7, 2021 •

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