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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,80 +1,193 @@ | ||
| // | ||
| // Prepare reference genome files | ||
| // Uncompress and prepare reference genome files | ||
| // | ||
|
|
||
| include { BEDTOOLS_MERGE } from '../../../modules/nf-core/bedtools/merge/main' | ||
| include { BEDTOOLS_SORT } from '../../../modules/nf-core/bedtools/sort/main' | ||
| include { CUSTOM_CATADDITIONALFASTA } from '../../../modules/nf-core/custom/catadditionalfasta' | ||
| include { CUSTOM_GETCHROMSIZES } from '../../../modules/nf-core/custom/getchromsizes' | ||
| include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' | ||
| include { GFFREAD } from '../../../modules/nf-core/gffread/main' | ||
| include { GTF2BED } from '../../../modules/local/gtf2bed' | ||
| include { GTF_FILTER } from '../../../modules/local/gtf_filter' | ||
| include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip' | ||
| include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip' | ||
| include { GUNZIP as GUNZIP_GENE_BED } from '../../../modules/nf-core/gunzip' | ||
| include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip' | ||
| include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip' | ||
| include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip' | ||
| include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' | ||
| include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' | ||
| include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' | ||
| include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' | ||
| include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' | ||
| include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/tabix/main' | ||
| include { UNTAR as UNTAR_STAR_INDEX } from '../../../modules/nf-core/untar' | ||
|
|
||
| workflow PREPARE_GENOME { | ||
| take: | ||
| ch_fasta_raw // file: /path/to/genome.fasta | ||
| ch_gff // file: /path/to/genome.gff | ||
| ch_gtf_raw // file: /path/to/genome.gtf | ||
| ch_dbsnp | ||
| ch_known_indels | ||
| feature_type | ||
| fasta // file: /path/to/genome.fasta | ||
| gtf // file: /path/to/genome.gtf | ||
| gff // file: /path/to/genome.gff | ||
| additional_fasta // file: /path/to/additional.fasta | ||
| transcript_fasta // file: /path/to/transcript.fasta | ||
| gene_bed // file: /path/to/gene.bed | ||
| dbsnp // file: /path/to/dbsnp.vcf | ||
| known_indels // file: /path/to/known_indels.vcf | ||
| star_index // directory: /path/to/star/index/ | ||
| featurecounts_group_type // string: The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts | ||
| gencode // boolean: whether the genome is from GENCODE | ||
| skip_gtf_filter // boolean: Skip filtering of GTF for valid scaffolds and/ or transcript IDs | ||
|
|
||
| main: | ||
| ch_versions = Channel.empty() | ||
|
|
||
| //Unzip reference genome files if needed | ||
|
|
||
| if (params.fasta.endsWith('.gz')) { | ||
| GUNZIP_FASTA(ch_fasta_raw) | ||
| // | ||
| // Uncompress genome fasta file if required | ||
| // | ||
| if (fasta.endsWith('.gz')) { | ||
| ch_fasta = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map { it[1] } | ||
| ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions) | ||
| } else { | ||
| ch_fasta = Channel.value(file(fasta)) | ||
| } | ||
|
|
||
| ch_fasta = GUNZIP_FASTA.out.gunzip | ||
| // | ||
| // Uncompress GTF annotation file or create from GFF3 if required | ||
| // | ||
| if (gtf || gff) { | ||
| if (gtf) { | ||
| if (gtf.endsWith('.gz')) { | ||
| ch_gtf = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map { it[1] } | ||
| ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) | ||
| } else { | ||
| ch_gtf = Channel.value(file(gtf)) | ||
| } | ||
| } else if (gff) { | ||
| if (gff.endsWith('.gz')) { | ||
| ch_gff = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map { it[1] } | ||
| ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions) | ||
| } else { | ||
| ch_gff = Channel.value(file(gff)) | ||
| } | ||
| ch_gtf = GFFREAD ( ch_gff ).gtf | ||
| ch_versions = ch_versions.mix(GFFREAD.out.versions) | ||
| } | ||
|
|
||
| } else { | ||
| ch_fasta = ch_fasta_raw | ||
| // Determine whether to filter the GTF or not | ||
| def filter_gtf = | ||
| (( | ||
| // Condition 1: Transcript FASTA file is not provided | ||
| !transcript_fasta | ||
| )) && | ||
| ( | ||
| // Condition 2: --skip_gtf_filter is not provided | ||
| !skip_gtf_filter | ||
| ) | ||
| if (filter_gtf) { | ||
| GTF_FILTER ( ch_fasta, ch_gtf ) | ||
| ch_gtf = GTF_FILTER.out.genome_gtf | ||
| ch_versions = ch_versions.mix(GTF_FILTER.out.versions) | ||
| } | ||
| } | ||
|
|
||
| if (params.gtf.endsWith('.gz')) { | ||
| GUNZIP_GTF(ch_gtf_raw) | ||
| // | ||
| // Uncompress additional fasta file and concatenate with reference fasta and gtf files | ||
| // | ||
| def biotype = gencode ? "gene_type" : featurecounts_group_type | ||
| if (additional_fasta) { | ||
| if (additional_fasta.endsWith('.gz')) { | ||
| ch_add_fasta = GUNZIP_ADDITIONAL_FASTA ( [ [:], additional_fasta ] ).gunzip.map { it[1] } | ||
| ch_versions = ch_versions.mix(GUNZIP_ADDITIONAL_FASTA.out.versions) | ||
| } else { | ||
| ch_add_fasta = Channel.value(file(additional_fasta)) | ||
| } | ||
|
|
||
| ch_gtf = GUNZIP_GTF.out.gunzip | ||
| CUSTOM_CATADDITIONALFASTA ( | ||
| ch_fasta.combine(ch_gtf).map { fasta, gtf -> [ [:], fasta, gtf ] }, | ||
| ch_add_fasta.map { [ [:], it ] }, | ||
| biotype | ||
| ) | ||
| ch_fasta = CUSTOM_CATADDITIONALFASTA.out.fasta.map { it[1] }.first() | ||
| ch_gtf = CUSTOM_CATADDITIONALFASTA.out.gtf.map { it[1] }.first() | ||
| ch_versions = ch_versions.mix(CUSTOM_CATADDITIONALFASTA.out.versions) | ||
| } | ||
|
|
||
| // | ||
| // Uncompress gene BED annotation file or create from GTF if required | ||
| // | ||
| if (gene_bed) { | ||
| if (gene_bed.endsWith('.gz')) { | ||
| ch_gene_bed = GUNZIP_GENE_BED ( [ [:], gene_bed ] ).gunzip.map { it[1] } | ||
| ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions) | ||
| } else { | ||
| ch_gene_bed = Channel.value(file(gene_bed)) | ||
| } | ||
| } else { | ||
| ch_gene_bed = GTF2BED ( ch_gtf ).bed | ||
| ch_versions = ch_versions.mix(GTF2BED.out.versions) | ||
| } | ||
|
|
||
| // | ||
| // Uncompress transcript fasta file / create if required | ||
| // | ||
| if (transcript_fasta) { | ||
| if (transcript_fasta.endsWith('.gz')) { | ||
| ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [ [:], transcript_fasta ] ).gunzip.map { it[1] } | ||
| ch_versions = ch_versions.mix(GUNZIP_TRANSCRIPT_FASTA.out.versions) | ||
| } else { | ||
| ch_transcript_fasta = Channel.value(file(transcript_fasta)) | ||
| } | ||
| if (gencode) { | ||
| PREPROCESS_TRANSCRIPTS_FASTA_GENCODE ( ch_transcript_fasta ) | ||
| ch_transcript_fasta = PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.fasta | ||
| ch_versions = ch_versions.mix(PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.versions) | ||
| } | ||
| } else { | ||
| ch_gtf = ch_gtf_raw | ||
| ch_transcript_fasta = MAKE_TRANSCRIPTS_FASTA ( ch_fasta, ch_gtf ).transcript_fasta | ||
| ch_versions = ch_versions.mix(MAKE_TRANSCRIPTS_FASTA.out.versions) | ||
| } | ||
|
|
||
| // | ||
| // Create chromosome sizes file | ||
| // | ||
| CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } ) | ||
| ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] } | ||
| ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] } | ||
| ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions) | ||
|
|
||
| GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) | ||
| GFFREAD(ch_gff, ch_fasta) | ||
| SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) | ||
| TABIX_DBSNP(ch_dbsnp.flatten().map{ it -> [ [ id:it.baseName ], it ] }) | ||
| TABIX_KNOWN_INDELS(ch_known_indels.flatten().map{ it -> [ [ id:it.baseName ], it ] } ) | ||
|
|
||
| ch_gtf = ch_gtf.mix(GFFREAD.out.gtf) | ||
|
|
||
| GTF2BED(ch_gtf, feature_type) | ||
| STAR_GENOMEGENERATE(ch_fasta, ch_gtf) | ||
|
|
||
| ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) | ||
| ch_versions = ch_versions.mix(GFFREAD.out.versions) | ||
| ch_versions = ch_versions.mix(GTF2BED.out.versions) | ||
| ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) | ||
| ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) | ||
| ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions) | ||
| ch_versions = ch_versions.mix(TABIX_KNOWN_INDELS.out.versions) | ||
|
|
||
| // | ||
| // Uncompress STAR index or generate from scratch if required | ||
| // | ||
| ch_star_index = Channel.empty() | ||
| if (star_index) { | ||
| if (star_index.endsWith('.tar.gz')) { | ||
| ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map { it[1] } | ||
| ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions) | ||
| } else { | ||
| ch_star_index = Channel.value(file(star_index)) | ||
| } | ||
| } else { | ||
| ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] } | ||
| ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) | ||
| } | ||
|
|
||
| emit: | ||
| dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict | ||
| exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed | ||
| fasta = ch_fasta | ||
| fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai | ||
| gtf = ch_gtf // path: genome.gtf | ||
| star_index = STAR_GENOMEGENERATE.out.index // path: star/index/ | ||
| chrom_sizes = ch_chrom_sizes // channel: path(genome.sizes) | ||
| dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi | ||
| dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict | ||
| fai = ch_fai // channel: path(genome.fai) | ||
| fasta = ch_fasta // channel: path(genome.fasta) | ||
| gene_bed = ch_gene_bed // channel: path(gene.bed) | ||
| gtf = ch_gtf // channel: path(genome.gtf) | ||
| known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi | ||
| versions = ch_versions // channel: [ versions.yml ] | ||
| // bedtools_sort = ch_bedtools_sort // path: sort.bed | ||
| // bedtools_merge = ch_bedtools_merge // path: merge.bed | ||
| star_index = ch_star_index // channel: path(star/index/) | ||
| transcript_fasta = ch_transcript_fasta // channel: path(transcript.fasta) | ||
| versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] | ||
| } |
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