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Fix GFFREAD #435

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merged 7 commits into from
Nov 26, 2024
Merged

Fix GFFREAD #435

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cb1317e
fix GFFREAD
ftabaro Nov 19, 2024
b775286
Implement meta.id detection for GFFREAD
ftabaro Nov 20, 2024
16bf0bc
remove whitespaces on line 74
ftabaro Nov 21, 2024
4aa51fe
use gff basename for meta.id calculation
ftabaro Nov 21, 2024
1abc2ff
implement suggestions
ftabaro Nov 25, 2024
2a05331
update CHANGELOG.md
ftabaro Nov 25, 2024
705797c
Merge branch 'dev' into fix-gffread
JoseEspinosa Nov 25, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,7 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

[[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
- [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
- [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.

### Parameters

Expand Down
108 changes: 56 additions & 52 deletions subworkflows/local/prepare_genome.nf
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Expand Up @@ -3,33 +3,35 @@
//

include {
GUNZIP as GUNZIP_FASTA
GUNZIP as GUNZIP_GTF
GUNZIP as GUNZIP_GFF
GUNZIP as GUNZIP_GENE_BED
GUNZIP as GUNZIP_BLACKLIST } from '../../modules/nf-core/gunzip/main'
GUNZIP as GUNZIP_FASTA ;
GUNZIP as GUNZIP_GTF ;
GUNZIP as GUNZIP_GFF ;
GUNZIP as GUNZIP_GENE_BED ;
GUNZIP as GUNZIP_BLACKLIST
} from '../../modules/nf-core/gunzip/main'

include {
UNTAR as UNTAR_BWA_INDEX
UNTAR as UNTAR_BOWTIE2_INDEX
UNTAR as UNTAR_STAR_INDEX } from '../../modules/nf-core/untar/main'

include { UNTARFILES } from '../../modules/nf-core/untarfiles/main'
include { GFFREAD } from '../../modules/nf-core/gffread/main'
include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main'
include { BWA_INDEX } from '../../modules/nf-core/bwa/index/main'
include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
include { CHROMAP_INDEX } from '../../modules/nf-core/chromap/index/main'

include { GTF2BED } from '../../modules/local/gtf2bed'
include { GENOME_BLACKLIST_REGIONS } from '../../modules/local/genome_blacklist_regions'
include { STAR_GENOMEGENERATE } from '../../modules/local/star_genomegenerate'
UNTAR as UNTAR_BWA_INDEX ;
UNTAR as UNTAR_BOWTIE2_INDEX ;
UNTAR as UNTAR_STAR_INDEX
} from '../../modules/nf-core/untar/main'

include { UNTARFILES } from '../../modules/nf-core/untarfiles/main'
include { GFFREAD } from '../../modules/nf-core/gffread/main'
include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main'
include { BWA_INDEX } from '../../modules/nf-core/bwa/index/main'
include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
include { CHROMAP_INDEX } from '../../modules/nf-core/chromap/index/main'

include { GTF2BED } from '../../modules/local/gtf2bed'
include { GENOME_BLACKLIST_REGIONS } from '../../modules/local/genome_blacklist_regions'
include { STAR_GENOMEGENERATE } from '../../modules/local/star_genomegenerate'

workflow PREPARE_GENOME {
take:
genome // string: genome name
genomes // map: genome attributes
prepare_tool_index // string : tool to prepare index for
prepare_tool_index // string: tool to prepare index for
fasta // path: path to genome fasta file
gtf // file: /path/to/genome.gtf
gff // file: /path/to/genome.gff
Expand All @@ -49,30 +51,32 @@ workflow PREPARE_GENOME {
//
ch_fasta = Channel.empty()
if (fasta.endsWith('.gz')) {
ch_fasta = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map{ it[1] }
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))
}
else {
ch_fasta = Channel.value(file(fasta, checkIfExists: true))
}

//
// Uncompress GTF annotation file or create from GFF3 if required
//
if (gtf) {
if (gtf.endsWith('.gz')) {
ch_gtf = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map{ it[1] }
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))
ch_gtf = Channel.value(file(gtf, checkIfExists: true))
}
} 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)
ch_gff = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions).map { [ [:], it ] }
} else {
ch_gff = Channel.value(file(gff))
ch_gff = Channel.value(file(gff, checkIfExists: true))
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}
ch_gtf = GFFREAD ( [ [:], ch_gff ] ).gtf

ch_gtf = GFFREAD(ch_gff, []).gtf.map { it[1] }
ch_versions = ch_versions.mix(GFFREAD.out.versions)
}

Expand All @@ -82,7 +86,7 @@ workflow PREPARE_GENOME {
ch_blacklist = Channel.empty()
if (blacklist) {
if (blacklist.endsWith('.gz')) {
ch_blacklist = GUNZIP_BLACKLIST ( [ [:], blacklist ] ).gunzip.map{ it[1] }
ch_blacklist = GUNZIP_BLACKLIST([[:], blacklist]).gunzip.map { it[1] }
ch_versions = ch_versions.mix(GUNZIP_BLACKLIST.out.versions)
} else {
ch_blacklist = Channel.value(file(blacklist))
Expand All @@ -99,17 +103,17 @@ workflow PREPARE_GENOME {
if (!gene_bed) {
make_bed = true
} else if (genome && gtf) {
if (genomes[ genome ].gtf != gtf) {
if (genomes[genome].gtf != gtf) {
make_bed = true
}
}

if (make_bed) {
ch_gene_bed = GTF2BED ( ch_gtf ).bed
ch_gene_bed = GTF2BED(ch_gtf).bed
ch_versions = ch_versions.mix(GTF2BED.out.versions)
} else {
if (gene_bed.endsWith('.gz')) {
ch_gene_bed = GUNZIP_GENE_BED ( [ [:], gene_bed ] ).gunzip.map{ it[1] }
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))
Expand All @@ -119,22 +123,22 @@ workflow PREPARE_GENOME {
//
// Create chromosome sizes file
//
CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } )
CUSTOM_GETCHROMSIZES(ch_fasta.map { [[:], it] })
ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map{ it[1] }
ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] }
ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)

//
// Prepare genome intervals for filtering by removing regions in blacklist file
//
ch_genome_filtered_bed = Channel.empty()

GENOME_BLACKLIST_REGIONS (
GENOME_BLACKLIST_REGIONS(
ch_chrom_sizes,
ch_blacklist.ifEmpty([])
)
ch_genome_filtered_bed = GENOME_BLACKLIST_REGIONS.out.bed
ch_versions = ch_versions.mix(GENOME_BLACKLIST_REGIONS.out.versions)
ch_versions = ch_versions.mix(GENOME_BLACKLIST_REGIONS.out.versions)

//
// Uncompress BWA index or generate from scratch if required
Expand All @@ -143,13 +147,13 @@ workflow PREPARE_GENOME {
if (prepare_tool_index == 'bwa') {
if (bwa_index) {
if (bwa_index.endsWith('.tar.gz')) {
ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], bwa_index ] ).untar
ch_bwa_index = UNTAR_BWA_INDEX([[:], bwa_index]).untar
ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
} else {
ch_bwa_index = [ [:], file(bwa_index) ]
ch_bwa_index = [[:], file(bwa_index)]
}
} else {
ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index
ch_bwa_index = BWA_INDEX(ch_fasta.map { [[:], it] }).index
ch_versions = ch_versions.mix(BWA_INDEX.out.versions)
}
}
Expand All @@ -161,13 +165,13 @@ workflow PREPARE_GENOME {
if (prepare_tool_index == 'bowtie2') {
if (bowtie2_index) {
if (bowtie2_index.endsWith('.tar.gz')) {
ch_bowtie2_index = UNTAR_BOWTIE2_INDEX ( [ [:], bowtie2_index ] ).untar
ch_versions = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
ch_bowtie2_index = UNTAR_BOWTIE2_INDEX([[:], bowtie2_index]).untar
ch_versions = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
} else {
ch_bowtie2_index = [ [:], file(bowtie2_index) ]
ch_bowtie2_index = [[:], file(bowtie2_index)]
}
} else {
ch_bowtie2_index = BOWTIE2_BUILD ( ch_fasta.map { [ [:], it ] } ).index
ch_bowtie2_index = BOWTIE2_BUILD(ch_fasta.map { [[:], it] }).index
ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions)
}
}
Expand All @@ -179,14 +183,14 @@ workflow PREPARE_GENOME {
if (prepare_tool_index == 'chromap') {
if (chromap_index) {
if (chromap_index.endsWith('.tar.gz')) {
ch_chromap_index = UNTARFILES ( [ [:], chromap_index ] ).files
ch_versions = ch_versions.mix(UNTARFILES.out.versions)
ch_chromap_index = UNTARFILES([[:], chromap_index]).files
ch_versions = ch_versions.mix(UNTARFILES.out.versions)
} else {
ch_chromap_index = [ [:], file(chromap_index) ]
ch_chromap_index = [[:], file(chromap_index)]
}
} else {
ch_chromap_index = CHROMAP_INDEX ( ch_fasta.map { [ [:], it ] } ).index
ch_versions = ch_versions.mix(CHROMAP_INDEX.out.versions)
ch_chromap_index = CHROMAP_INDEX(ch_fasta.map { [[:], it] }).index
ch_versions = ch_versions.mix(CHROMAP_INDEX.out.versions)
}
}

Expand All @@ -197,13 +201,13 @@ workflow PREPARE_GENOME {
if (prepare_tool_index == 'star') {
if (star_index) {
if (star_index.endsWith('.tar.gz')) {
ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map{ it[1] }
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, ch_gtf ).index
ch_star_index = STAR_GENOMEGENERATE(ch_fasta, ch_gtf).index
ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
}
}
Expand All @@ -219,5 +223,5 @@ workflow PREPARE_GENOME {
bowtie2_index = ch_bowtie2_index // path: bowtie2/index/
chromap_index = ch_chromap_index // path: genome.index
star_index = ch_star_index // path: star/index/
versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
}