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add argument extreme_sensistity to fusioninspector #424

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merged 2 commits into from
Oct 20, 2023
Merged

add argument extreme_sensistity to fusioninspector #424

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7275d6e
add argument extreme_sensistity to fusioninspector
rannick Oct 20, 2023
0c471d1
update changelog
rannick Oct 20, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389)
- Now publishing convert2bed output to convert2bed to keep the output file for mosdepth [#420](https://github.com/nf-core/rnafusion/pull/420)
- No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420)
- `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424)

### Fixed

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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -102,7 +102,7 @@ process {
withName: FUSIONINSPECTOR {
ext.when = { !params.skip_vis }
ext.args = { params.fusioninspector_limitSjdbInsertNsj != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' }

ext.args2 = '--extreme_sensitivity'
}

withName: FUSIONREPORT {
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3 changes: 2 additions & 1 deletion modules/local/fusioninspector/main.nf
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Expand Up @@ -21,6 +21,7 @@ process FUSIONINSPECTOR {
def prefix = task.ext.prefix ?: "${meta.id}"
def fasta = meta.single_end ? "--left_fq ${reads[0]}" : "--left_fq ${reads[0]} --right_fq ${reads[1]}"
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
"""
FusionInspector \\
--fusions $fusion_list \\
Expand All @@ -29,7 +30,7 @@ process FUSIONINSPECTOR {
--CPU ${task.cpus} \\
-O . \\
--out_prefix $prefix \\
--vis $args
--vis $args $args2

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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