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transcriptome_fasta -> transcript_fasta #97

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merged 1 commit into from Jun 10, 2022
Merged

transcriptome_fasta -> transcript_fasta #97

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8 changes: 4 additions & 4 deletions subworkflows/local/alevin.nf
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Expand Up @@ -27,9 +27,9 @@ workflow SCRNASEQ_ALEVIN {
main:
ch_versions = Channel.empty()

assert salmon_index || (genome_fasta && gtf) || (genome_fasta && transcriptome_fasta):
assert salmon_index || (genome_fasta && gtf) || (genome_fasta && transcript_fasta):
"""Must provide a genome fasta file ('--genome_fasta') and a gtf file ('--gtf'), or a genome fasta file
and a transcriptome fasta file ('--transcriptome_fasta`) if no index is given!""".stripIndent()
and a transcriptome fasta file ('--transcript_fasta`) if no index is given!""".stripIndent()

assert txp2gene || gtf:
"Must provide either a GTF file ('--gtf') or kallisto gene map ('--kallisto_gene_map') to align with kallisto bustools!"
Expand All @@ -42,10 +42,10 @@ workflow SCRNASEQ_ALEVIN {
// Preprocessing - Extract transcriptome fasta from genome fasta
if (!transcript_fasta) {
GFFREAD_TRANSCRIPTOME( genome_fasta, gtf )
transcriptome_fasta = GFFREAD_TRANSCRIPTOME.out.transcriptome_extracted
transcript_fasta = GFFREAD_TRANSCRIPTOME.out.transcriptome_extracted
ch_versions = ch_versions.mix(GFFREAD_TRANSCRIPTOME.out.versions)
}
SALMON_INDEX( genome_fasta, transcriptome_fasta )
SALMON_INDEX( genome_fasta, transcript_fasta )
salmon_index = SALMON_INDEX.out.index.collect()
ch_versions = ch_versions.mix(SALMON_INDEX.out.versions)
}
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