diff --git a/CHANGELOG.md b/CHANGELOG.md index b2ddfa6a..71393afc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Move from ensembl to gencode base [#505](https://github.com/nf-core/rnafusion/pull/505) - Update from ensembl 102 to gencode 46 default references [#505](https://github.com/nf-core/rnafusion/pull/505) - Update`FUSIONINSPECTOR` to v2.10.0. [#601](https://github.com/nf-core/rnafusion/pull/601) +- Remove local module `STARFUSION_DOWNLOAD` [#598](https://github.com/nf-core/rnafusion/pull/598) ### Fixed diff --git a/conf/modules.config b/conf/modules.config index c747fda7..69611e8a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -371,16 +371,6 @@ process { ext.args = "--max_readlength ${params.read_length} --human_gencode_filter" } - withName: 'STARFUSION_DOWNLOAD' { - cpus = { 2 * task.attempt } - memory = { 24.GB * task.attempt } - time = { 6.h * task.attempt } - publishDir = [ - path: { "${params.genomes_base}/starfusion" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] - } withName: 'STRINGTIE_MERGE' { publishDir = [ diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml deleted file mode 100644 index ef7f9316..00000000 --- a/modules/local/starfusion/download/environment.yml +++ /dev/null @@ -1,8 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::dfam=3.7 - - bioconda::hmmer=3.4 - - bioconda::minimap2=2.28 - - bioconda::star-fusion=1.14.0 diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf deleted file mode 100644 index ace18a9e..00000000 --- a/modules/local/starfusion/download/main.nf +++ /dev/null @@ -1,34 +0,0 @@ -process STARFUSION_DOWNLOAD { - tag 'star-fusion' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' : - 'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}" - - output: - path "ctat_genome_lib_build_dir/*" , emit: reference - - - // TODO: move to S3 - script: - """ - wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz --no-check-certificate - - tar xvf GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz - - rm GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz - - mv */ctat_genome_lib_build_dir . - """ - - stub: - """ - mkdir ctat_genome_lib_build_dir - touch ref_annot.cdna.fa - cat <<-END_VERSIONS > versions.yml - "${task.process}": - STAR-Fusion: \$(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //') - END_VERSIONS - """ -} diff --git a/modules/local/starfusion/download/meta.yml b/modules/local/starfusion/download/meta.yml deleted file mode 100644 index 24e84252..00000000 --- a/modules/local/starfusion/download/meta.yml +++ /dev/null @@ -1,25 +0,0 @@ -name: starfusion_downloadgenome -description: Download STAR-fusion genome resource required to run STAR-Fusion caller -keywords: - - downoad -tools: - - star-fusion: - description: Fusion calling algorithm for RNAseq data - homepage: https://github.com/STAR-Fusion/ - documentation: https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion - tool_dev_url: https://github.com/STAR-Fusion/STAR-Fusion - doi: "10.1186/s13059-019-1842-9" - licence: ["GPL v3"] - -output: - - reference: - type: directory - description: Genome resource path - pattern: "star-fusion-genome" - - gtf: - type: file - description: genome gtf file - pattern: "*.{gtf}" - -authors: - - "@praveenraj2018,@rannick"