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fix starfusion download output for gtf to refflat #463

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fix starfusion download output for gtf to refflat #463

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98f02be
Merge pull request #453 from nf-core/dev
fevac Nov 29, 2023
392698c
fix starfusion download output for gtf to refflat
dodslaser Jan 26, 2024
3ebff10
Merge branch 'dev' into fix_starfusion_download
rannick Jan 31, 2024
39f066c
Merge branch 'dev' into fix_starfusion_download
rannick Feb 29, 2024
96d4b78
Merge branch 'nf-core:master' into fix_starfusion_download
dodslaser Mar 19, 2024
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7 changes: 5 additions & 2 deletions modules/local/starfusion/download/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,12 @@ process STARFUSION_DOWNLOAD {
conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::trinity=2.13.2 bioconda::samtools=1.9 bioconda::star=2.7.8a"
container 'docker.io/trinityctat/starfusion:1.12.0'

input:
val meta

output:
path "ctat_genome_lib_build_dir/*" , emit: reference
path "ctat_genome_lib_build_dir/ref_annot.gtf", emit: chrgtf
path "ctat_genome_lib_build_dir/*" , emit: reference
tuple val(meta), path("ctat_genome_lib_build_dir/ref_annot.gtf"), emit: chrgtf


script:
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2 changes: 1 addition & 1 deletion workflows/build_references.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ workflow BUILD_REFERENCES {
if (params.starfusion_build){
STARFUSION_BUILD( ENSEMBL_DOWNLOAD.out.fasta, ENSEMBL_DOWNLOAD.out.chrgtf )
} else {
STARFUSION_DOWNLOAD()
STARFUSION_DOWNLOAD( fake_meta )
}
}

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