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SortMeRNA low mem params #105

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SortMeRNA low mem params #105

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235e008
Merge pull request #95 from nf-core/dev
pinin4fjords Feb 3, 2025
872054e
changed sortMeRNA params to not look for best alignment of rRNA reads…
JackCurragh Apr 30, 2025
8c4ea4d
update nextflow_schema.json and schema_input.json
andreirie Mar 26, 2025
bf47009
update nextflow_schema.json
andreirie Mar 26, 2025
3d5ac8a
Bump changelog
andreirie Mar 26, 2025
880ffd3
update nextflow_schema.json
andreirie Mar 26, 2025
71919b3
bump changelog
andreirie Mar 26, 2025
66a4049
updated changelog
JackCurragh Apr 30, 2025
20f5bfe
Merge branch 'dev' into sortMeRNA_low_mem_params
JackCurragh Apr 30, 2025
3feb510
bump Cache pdiff actions/cache to v4 due to CI complaint
JackCurragh May 7, 2025
4962134
remove empty line in CHANGELOG.md
JackCurragh May 7, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ jobs:
mkdir -p $NXF_SINGULARITY_LIBRARYDIR

- name: Cache pdiff
uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
uses: actions/cache@v4 # v4
id: cache-pip-pdiff
with:
path: ~/.cache/pip
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Changed`

- [#103](https://github.com/nf-core/riboseq/pull/103) - Updated the JSON schema to make input validation stricter([@andreirie](https://github.com/andreirie))
- [#104](https://github.com/nf-core/riboseq/pull/104) - Updated SortMeRNA params to lower memory usage by not looking for best alignment [@jackcurragh](https://github.com/jackcurragh)

### `Fixed`

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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -357,7 +357,7 @@ if (!params.skip_bbsplit) {
if (params.remove_ribo_rna) {
process {
withName: '.*:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA' {
ext.args = '--num_alignments 1 -v --index 0'
ext.args = '--no-best -v --index 0'
publishDir = [
[
path: { "${params.outdir}/preprocessing/sortmerna" },
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