New module ctat splicing #587

nvnieuwk · 2024-12-17T13:30:38Z

Adds CTAT-SPLICING on STARFUSION output. For now this module is a local module because of issues with creating the bioconda recipe. I hope this can be resolved some time in the future

TODOS:

Fully test this on real data

nf-core-bot · 2024-12-17T13:31:15Z

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Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
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github-actions · 2024-12-17T13:32:32Z

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

Posted for pipeline commit a209fea

+| ✅ 222 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

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nextflow_config - Found nf-schema plugin
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nextflow_config - Config timeline.enabled had correct value: true
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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 default value correct: params.ensembl_version= 102
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readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
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schema_lint - Schema lint passed
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modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_FOR_STARFUSION found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_FOR_STARFUSION_CRAM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_FOR_STARFUSION found in conf/modules.config and Nextflow scripts.
modules_config - STAR_FOR_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - STAR_FOR_STARFUSION found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_RNAFUSION found in conf/modules.config and Nextflow scripts.
modules_config - STARFUSION_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - STRINGTIE_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_GTFTOGENEPRED found in conf/modules.config and Nextflow scripts.
modules_config - VCF_COLLECT found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-12-20 10:53:24

nextflow.config

rannick

Looks great! Let me know when you are finished testing and I can make the last review

Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com>

nvnieuwk · 2024-12-17T13:42:49Z

Looks great! Let me know when you are finished testing and I can make the last review

Thanks! I started the test on our HPC, I'll keep you updated

rannick · 2024-12-17T13:44:05Z

Please also update the changelog 😄

nvnieuwk · 2024-12-17T13:47:20Z

Please also update the changelog 😄

Oh right I always forget that! 😁

…on into new-module-ctat-splicing

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

rannick

We need to keep the doc updated as well, since you know the tool the best, could you please do it? In this PR or another is fine by me

CHANGELOG.md

modules/local/ctatsplicing/startocancerintrons/main.nf

subworkflows/local/starfusion_workflow.nf

rannick

LGTM (just needs the tests passing)

nvnieuwk added 3 commits December 17, 2024 13:42

fix test config resources

dbb45c9

add ctatsplicing module

4245c54

implement ctatsplicing

f025945

fix pre-commit

3268a45

rannick self-requested a review December 17, 2024 13:36

rannick reviewed Dec 17, 2024

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nextflow.config Outdated Show resolved Hide resolved

rannick reviewed Dec 17, 2024

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Update nextflow.config

a84033b

Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com>

nvnieuwk added 8 commits December 17, 2024 14:48

update changelog

4247b12

Merge branch 'new-module-ctat-splicing' of github.com:nf-core/rnafusi…

af80d58

…on into new-module-ctat-splicing

make ctatsplicing possible with arriba input

0db19d9

add some views to debug the full run

350de1b

try to fix issue with arriba output

b8bae77

remove views

0006394

remove breaking ifEmpties

05e0e61

remove def

62fdf33

rannick reviewed Dec 19, 2024

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nvnieuwk and others added 6 commits December 19, 2024 16:03

redo star changes

8155168

use bam from starfusion

e386c81

create junctions with arriba for ctatsplicing

62ee76f

do not create an index in ctat splicing

19d1cc1

readd indexing to ctat & sort arriba bam

9dc352f

Merge branch 'dev' into new-module-ctat-splicing

45e4879

nvnieuwk marked this pull request as ready for review December 20, 2024 08:14

nvnieuwk requested a review from rannick December 20, 2024 08:14

rannick requested changes Dec 20, 2024

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nvnieuwk added 3 commits December 20, 2024 11:32

remove ctatsplicing check from starfusion

9ea1f3b

clarify changelog

1c98fc7

update docs

74d4534

rannick approved these changes Dec 20, 2024

View reviewed changes

prettyyy

a209fea

nvnieuwk merged commit 3f4406a into dev Dec 20, 2024
8 checks passed

nvnieuwk deleted the new-module-ctat-splicing branch December 20, 2024 12:33

rannick mentioned this pull request Dec 20, 2024

new module: CTAT/SPLICING #538

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New module ctat splicing #587

New module ctat splicing #587

nvnieuwk commented Dec 17, 2024

nf-core-bot commented Dec 17, 2024

github-actions bot commented Dec 17, 2024 •

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❔ Tests ignored:

✅ Tests passed:

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rannick commented Dec 17, 2024

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New module ctat splicing #587

New module ctat splicing #587

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nvnieuwk commented Dec 17, 2024

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nf-core pipelines lint overall result: Passed ✅

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✅ Tests passed:

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

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