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Fix ref build #420

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merged 5 commits into from
Oct 20, 2023
Merged

Fix ref build #420

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121e9df
change default input samplesheet to test one insead of fake file as n…
rannick Oct 2, 2023
897a544
make input existence not mendatory, so building references does not r…
rannick Oct 18, 2023
b21b4aa
add publishing directory for convert2bed files
rannick Oct 18, 2023
81118ed
update fusionreport
rannick Oct 18, 2023
fffb37b
update changelog
rannick Oct 20, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,10 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed

- 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)

### Fixed

- Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416)
- Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420)

### Removed

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13 changes: 8 additions & 5 deletions conf/modules.config
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Expand Up @@ -45,6 +45,14 @@ process {
]
}

withName: CONVERT2BED {
publishDir = [
path: { "${params.genomes_base}/convert2bed" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: CUSTOM_DUMPSOFTWAREVERSIONS {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
Expand Down Expand Up @@ -178,11 +186,6 @@ process {
ext.when = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)}
}

withName: REFORMAT {
ext.args = "forcetrimright=75"
ext.args2 = "forcetrimleft=75"
}

withName: SAMPLESHEET_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
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2 changes: 1 addition & 1 deletion modules/local/fusionreport/detect/main.nf
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Expand Up @@ -4,7 +4,7 @@ process FUSIONREPORT {

// Note: 2.7X indices incompatible with AWS iGenomes.
conda "bioconda::star=2.7.9a"
container "docker.io/clinicalgenomics/fusion-report:2.1.5p4"
container "docker.io/clinicalgenomics/fusion-report:2.1.5p5"


input:
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2 changes: 1 addition & 1 deletion modules/local/fusionreport/download/main.nf
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Expand Up @@ -4,7 +4,7 @@ process FUSIONREPORT_DOWNLOAD {

// Note: 2.7X indices incompatible with AWS iGenomes.
conda "bioconda::star=2.7.9a"
container "docker.io/clinicalgenomics/fusion-report:2.1.5p4"
container "docker.io/clinicalgenomics/fusion-report:2.1.5p5"

input:
val(username)
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1 change: 0 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -32,7 +32,6 @@
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
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