From edc1a42d47f36814b1c5cf9af91ba5b46acd5de4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 12:42:42 +0100 Subject: [PATCH 1/3] update arriba --- CHANGELOG.md | 1 + modules/local/arriba/download/main.nf | 20 ++++++++++---------- modules/local/arriba/visualisation/main.nf | 6 +++--- nextflow.config | 8 ++++---- 4 files changed, 18 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a071696..0e74c70b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 ### Fixed diff --git a/modules/local/arriba/download/main.nf b/modules/local/arriba/download/main.nf index 166ed69f..d59c123b 100644 --- a/modules/local/arriba/download/main.nf +++ b/modules/local/arriba/download/main.nf @@ -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/v2.3.0/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 "${task.process}": @@ -27,11 +27,11 @@ process ARRIBA_DOWNLOAD { stub: """ - touch blacklist_hg38_GRCh38_v2.3.0.tsv.gz - touch protein_domains_hg38_GRCh38_v2.3.0.gff3 - touch cytobands_hg38_GRCh38_v2.3.0.tsv - touch known_fusions_hg38_GRCh38_v2.3.0.tsv.gz - touch protein_domains_hg38_GRCh38_v2.3.0.gff3 + touch blacklist_hg38_GRCh38_v2.4.0.tsv.gz + touch protein_domains_hg38_GRCh38_v2.4.0.gff3 + touch cytobands_hg38_GRCh38_v2.4.0.tsv + touch known_fusions_hg38_GRCh38_v2.4.0.tsv.gz + touch protein_domains_hg38_GRCh38_v2.4.0.gff3 cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/arriba/visualisation/main.nf b/modules/local/arriba/visualisation/main.nf index 5805a904..cc120119 100644 --- a/modules/local/arriba/visualisation/main.nf +++ b/modules/local/arriba/visualisation/main.nf @@ -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) diff --git a/nextflow.config b/nextflow.config index 925d7a36..5f1e3c2c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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" From 0b4f60f6789c9ef1b1275aeb5f15f1a79f746644 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 17:09:47 +0100 Subject: [PATCH 2/3] fix typo --- modules/local/arriba/download/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/arriba/download/main.nf b/modules/local/arriba/download/main.nf index d59c123b..860439ad 100644 --- a/modules/local/arriba/download/main.nf +++ b/modules/local/arriba/download/main.nf @@ -13,7 +13,7 @@ process ARRIBA_DOWNLOAD { script: """ - wget https://github.com/suhrig/arriba/releases/download/v2.3.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz + 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/* . From a641b172522408cae7060e5b2b22ed1b65f773ed Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 21:47:17 +0100 Subject: [PATCH 3/3] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e74c70b..c9dcad59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +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 +- `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) ### Fixed