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Update subworkflow to account for fix to bad argument handling #1470

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merged 4 commits into from
Dec 18, 2024
Merged

Update subworkflow to account for fix to bad argument handling #1470

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68d4e81
Update subworkflow to account for fix to bad argument handling
pinin4fjords Dec 17, 2024
ca92fe7
Update changelog
pinin4fjords Dec 17, 2024
81f2824
Merge branch 'dev' into fix_prepro_arg
pinin4fjords Dec 17, 2024
11b8670
Merge branch 'dev' into fix_prepro_arg
pinin4fjords Dec 18, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ Special thanks to the following for their contributions to the release:
- [PR #1463](https://github.com/nf-core/rnaseq/pull/1463) - Move channel operations outside of the onComplete() block
- [PR #1467](https://github.com/nf-core/rnaseq/pull/1467) - Add test suite for UMI handling functionality
- [PR #1466](https://github.com/nf-core/rnaseq/pull/1466) - Factor out UMI handling
- [PR #1470](https://github.com/nf-core/rnaseq/pull/1470) - Update subworkflow to account for fix to bad argument handling
- [PR #1469](https://github.com/nf-core/rnaseq/pull/1469) - Minor docs fix
- [PR #1459](https://github.com/nf-core/rnaseq/pull/1466) - Remove reference to unused "skip_sample_count" value in email templates

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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -363,7 +363,7 @@
},
"fastq_qc_trim_filter_setstrandedness": {
"branch": "master",
"git_sha": "2c0260ed80daeca9c6dfa477a4daf04ff336dc37",
"git_sha": "8a01490596dbe8443bd6bc6ae4207ae9485f33e3",
"installed_by": ["subworkflows"]
},
"fastq_subsample_fq_salmon": {
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3 changes: 2 additions & 1 deletion subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
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4 changes: 4 additions & 0 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml
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2 changes: 2 additions & 0 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test
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3 changes: 2 additions & 1 deletion workflows/rnaseq/main.nf
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Expand Up @@ -155,7 +155,8 @@ workflow RNASEQ {
params.umi_discard_read,
params.stranded_threshold,
params.unstranded_threshold,
params.skip_linting
params.skip_linting,
false
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@maxulysse maxulysse Dec 17, 2024 •
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no params for this?
Just false always?

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I don't really know why it's a module input, I don't think it's a core behaviour of FASTP. I'm struggling to see the use case for it to justify adding a pipeline param and wiring it in.

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Though I can if you really want...

)

ch_multiqc_files = ch_multiqc_files.mix(FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.out.multiqc_files)
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