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update arriba #429

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merged 3 commits into from
Nov 7, 2023
Merged

update arriba #429

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edc1a42
update arriba
rannick Nov 6, 2023
0b4f60f
fix typo
rannick Nov 6, 2023
a641b17
update changelog
rannick Nov 6, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- 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)
- `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426)
- `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429)

### Fixed

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20 changes: 10 additions & 10 deletions modules/local/arriba/download/main.nf
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Expand Up @@ -13,11 +13,11 @@ process ARRIBA_DOWNLOAD {

script:
"""
wget https://github.com/suhrig/arriba/releases/download/v2.3.0/arriba_v2.3.0.tar.gz -O arriba_v2.3.0.tar.gz
tar -xzvf arriba_v2.3.0.tar.gz
rm arriba_v2.3.0.tar.gz
mv arriba_v2.3.0/database/* .
rm -r arriba_v2.3.0
wget https://github.com/suhrig/arriba/releases/download/v2.4.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz
tar -xzvf arriba_v2.4.0.tar.gz
rm arriba_v2.4.0.tar.gz
mv arriba_v2.4.0/database/* .
rm -r arriba_v2.4.0

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -27,11 +27,11 @@ process ARRIBA_DOWNLOAD {

stub:
"""
touch blacklist_hg38_GRCh38_v2.3.0.tsv.gz
touch protein_domains_hg38_GRCh38_v2.3.0.gff3
touch cytobands_hg38_GRCh38_v2.3.0.tsv
touch known_fusions_hg38_GRCh38_v2.3.0.tsv.gz
touch protein_domains_hg38_GRCh38_v2.3.0.gff3
touch blacklist_hg38_GRCh38_v2.4.0.tsv.gz
touch protein_domains_hg38_GRCh38_v2.4.0.gff3
touch cytobands_hg38_GRCh38_v2.4.0.tsv
touch known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
touch protein_domains_hg38_GRCh38_v2.4.0.gff3

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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6 changes: 3 additions & 3 deletions modules/local/arriba/visualisation/main.nf
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Expand Up @@ -2,10 +2,10 @@ process ARRIBA_VISUALISATION {
tag "$meta.id"
label 'process_medium'

conda "bioconda::arriba=2.3.0"
conda "bioconda::arriba=2.4.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' :
'quay.io/biocontainers/arriba:2.3.0--haa8aa89_0' }"
'https://depot.galaxyproject.org/singularity/arriba:2.4.0--h0033a41_2' :
'biocontainers/arriba:2.4.0--h0033a41_2' }"

input:
tuple val(meta), path(bam), path(bai), path(fusions)
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8 changes: 4 additions & 4 deletions nextflow.config
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Expand Up @@ -66,10 +66,10 @@ params {
// Path to references
ensembl_ref = "${params.genomes_base}/ensembl"
arriba_ref = "${params.genomes_base}/arriba"
arriba_ref_blacklist = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.3.0.tsv.gz"
arriba_ref_cytobands = "${params.genomes_base}/arriba/cytobands_hg38_GRCh38_v2.3.0.tsv"
arriba_ref_known_fusions = "${params.genomes_base}/arriba/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz"
arriba_ref_protein_domains = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.3.0.gff3"
arriba_ref_blacklist = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz"
arriba_ref_cytobands = "${params.genomes_base}/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv"
arriba_ref_known_fusions = "${params.genomes_base}/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz"
arriba_ref_protein_domains = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3"
fusioncatcher_ref = "${params.genomes_base}/fusioncatcher/human_v102"
starfusion_ref = "${params.genomes_base}/starfusion/ctat_genome_lib_build_dir"
starindex_ref = "${params.genomes_base}/star"
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