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Fix --blacklist error and make fasta always available for IGV #291

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merged 3 commits into from
Jun 9, 2023
Merged

Fix --blacklist error and make fasta always available for IGV #291

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9f7d061
Make fasta genome file available by default for IGV
JoseEspinosa Jun 9, 2023
b7026cb
Fix issue with blacklist provided using the blacklist param
JoseEspinosa Jun 9, 2023
8f0d882
Update changelog
JoseEspinosa Jun 9, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Add public_aws_ecr profile for using containers hosted on ECR.
- [[#277](https://github.com/nf-core/atacseq/issues/277)] - Fix error when using a gunziped fasta file.
- [[#286](https://github.com/nf-core/atacseq/issues/286)] - Fix error when no `--mito_name parameter is provided.
- [[#268](https://github.com/nf-core/atacseq/issues/268)] - Fix error when a bed file is provided using the `--blacklist` option.
- [[#278](https://github.com/nf-core/atacseq/issues/278)] - Make genome fasta file available when `IGV` process is run.

### Parameters

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3 changes: 1 addition & 2 deletions conf/modules.config
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Expand Up @@ -957,8 +957,7 @@ if (!params.skip_igv) {
[
path: { "${params.outdir}/genome" },
mode: params.publish_dir_mode,
pattern: '*.{fa,fasta}',
enabled: params.save_reference
pattern: '*.{fa,fasta}'
]
]
}
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8 changes: 4 additions & 4 deletions subworkflows/local/prepare_genome.nf
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Expand Up @@ -77,7 +77,7 @@ workflow PREPARE_GENOME {
ch_blacklist = GUNZIP_BLACKLIST ( [ [:], params.blacklist ] ).gunzip.map{ it[1] }
ch_versions = ch_versions.mix(GUNZIP_BLACKLIST.out.versions)
} else {
ch_blacklist = Channel.of(params.blacklist)
ch_blacklist = Channel.value(file(params.blacklist))
}
}

Expand All @@ -104,7 +104,7 @@ workflow PREPARE_GENOME {
ch_gene_bed = GUNZIP_GENE_BED ( [ [:], params.gene_bed ] ).gunzip.map{ it[1] }
ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions)
} else {
ch_gene_bed = file(params.gene_bed)
ch_gene_bed = Channel.value(file(params.gene_bed))
}
}

Expand All @@ -116,7 +116,7 @@ workflow PREPARE_GENOME {
ch_tss_bed = GUNZIP_TSS_BED ( [ [:], params.tss_bed ] ).gunzip.map{ it[1] }
ch_versions = ch_versions.mix(GUNZIP_TSS_BED.out.versions)
} else {
ch_tss_bed = file(params.tss_bed)
ch_tss_bed = Channel.value(file(params.tss_bed))
}
}

Expand Down Expand Up @@ -216,7 +216,7 @@ workflow PREPARE_GENOME {
ch_star_index = UNTAR_STAR_INDEX ( [ [:], params.star_index ] ).untar.map{ it[1] }
ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
} else {
ch_star_index = file(params.star_index)
ch_star_index = Channel.value(file(params.star_index))
}
} else {
ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index
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