Skip to content

Commit 1abc2ff

Browse files
ftabaroftabaro
committed
implement suggestions
1 parent 4aa51fe commit 1abc2ff

File tree

1 file changed

+43
-65
lines changed

1 file changed

+43
-65
lines changed

‎subworkflows/local/prepare_genome.nf‎

Lines changed: 43 additions & 65 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ workflow PREPARE_GENOME {
3131
take:
3232
genome // string: genome name
3333
genomes // map: genome attributes
34-
prepare_tool_index // string : tool to prepare index for
34+
prepare_tool_index // string: tool to prepare index for
3535
fasta // path: path to genome fasta file
3636
gtf // file: /path/to/genome.gtf
3737
gff // file: /path/to/genome.gff
@@ -51,7 +51,7 @@ workflow PREPARE_GENOME {
5151
//
5252
ch_fasta = Channel.empty()
5353
if (fasta.endsWith('.gz')) {
54-
ch_fasta = GUNZIP_FASTA([[:], fasta]).gunzip.map { it[1] }
54+
ch_fasta = GUNZIP_FASTA([[:], fasta]).gunzip.map { it[1] }
5555
ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
5656
}
5757
else {
@@ -63,30 +63,20 @@ workflow PREPARE_GENOME {
6363
//
6464
if (gtf) {
6565
if (gtf.endsWith('.gz')) {
66-
ch_gtf = GUNZIP_GTF([[:], gtf]).gunzip.map { it[1] }
66+
ch_gtf = GUNZIP_GTF([[:], gtf]).gunzip.map { it[1] }
6767
ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
68-
}
69-
else {
68+
} else {
7069
ch_gtf = Channel.value(file(gtf, checkIfExists: true))
7170
}
72-
}
73-
else if (gff) {
71+
} else if (gff) {
7472
if (gff.endsWith('.gz')) {
75-
ch_gff = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
76-
ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
77-
}
78-
else {
73+
ch_gff = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
74+
ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions).map { [ [:], it ] }
75+
} else {
7976
ch_gff = Channel.value(file(gff, checkIfExists: true))
8077
}
8178

82-
//
83-
// Detect gff file name stripped of extension and .gz
84-
//
85-
extension = (gff - '.gz').tokenize('.')[-1]
86-
id = file(gff).baseName.toString() - '.gz' - ".${extension}"
87-
88-
ch_gtf = GFFREAD(ch_gff.map { [[id: id], it] }, []).gtf.map { it[1] }
89-
79+
ch_gtf = GFFREAD(ch_gff, []).gtf.map { it[1] }
9080
ch_versions = ch_versions.mix(GFFREAD.out.versions)
9181
}
9282

@@ -97,9 +87,8 @@ workflow PREPARE_GENOME {
9787
if (blacklist) {
9888
if (blacklist.endsWith('.gz')) {
9989
ch_blacklist = GUNZIP_BLACKLIST([[:], blacklist]).gunzip.map { it[1] }
100-
ch_versions = ch_versions.mix(GUNZIP_BLACKLIST.out.versions)
101-
}
102-
else {
90+
ch_versions = ch_versions.mix(GUNZIP_BLACKLIST.out.versions)
91+
} else {
10392
ch_blacklist = Channel.value(file(blacklist))
10493
}
10594
}
@@ -113,8 +102,7 @@ workflow PREPARE_GENOME {
113102
def make_bed = false
114103
if (!gene_bed) {
115104
make_bed = true
116-
}
117-
else if (genome && gtf) {
105+
} else if (genome && gtf) {
118106
if (genomes[genome].gtf != gtf) {
119107
make_bed = true
120108
}
@@ -123,13 +111,11 @@ workflow PREPARE_GENOME {
123111
if (make_bed) {
124112
ch_gene_bed = GTF2BED(ch_gtf).bed
125113
ch_versions = ch_versions.mix(GTF2BED.out.versions)
126-
}
127-
else {
114+
} else {
128115
if (gene_bed.endsWith('.gz')) {
129116
ch_gene_bed = GUNZIP_GENE_BED([[:], gene_bed]).gunzip.map { it[1] }
130117
ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions)
131-
}
132-
else {
118+
} else {
133119
ch_gene_bed = Channel.value(file(gene_bed))
134120
}
135121
}
@@ -139,8 +125,8 @@ workflow PREPARE_GENOME {
139125
//
140126
CUSTOM_GETCHROMSIZES(ch_fasta.map { [[:], it] })
141127
ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
142-
ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] }
143-
ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
128+
ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] }
129+
ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
144130

145131
//
146132
// Prepare genome intervals for filtering by removing regions in blacklist file
@@ -152,7 +138,7 @@ workflow PREPARE_GENOME {
152138
ch_blacklist.ifEmpty([])
153139
)
154140
ch_genome_filtered_bed = GENOME_BLACKLIST_REGIONS.out.bed
155-
ch_versions = ch_versions.mix(GENOME_BLACKLIST_REGIONS.out.versions)
141+
ch_versions = ch_versions.mix(GENOME_BLACKLIST_REGIONS.out.versions)
156142

157143
//
158144
// Uncompress BWA index or generate from scratch if required
@@ -162,15 +148,13 @@ workflow PREPARE_GENOME {
162148
if (bwa_index) {
163149
if (bwa_index.endsWith('.tar.gz')) {
164150
ch_bwa_index = UNTAR_BWA_INDEX([[:], bwa_index]).untar
165-
ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
166-
}
167-
else {
151+
ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
152+
} else {
168153
ch_bwa_index = [[:], file(bwa_index)]
169154
}
170-
}
171-
else {
155+
} else {
172156
ch_bwa_index = BWA_INDEX(ch_fasta.map { [[:], it] }).index
173-
ch_versions = ch_versions.mix(BWA_INDEX.out.versions)
157+
ch_versions = ch_versions.mix(BWA_INDEX.out.versions)
174158
}
175159
}
176160

@@ -182,15 +166,13 @@ workflow PREPARE_GENOME {
182166
if (bowtie2_index) {
183167
if (bowtie2_index.endsWith('.tar.gz')) {
184168
ch_bowtie2_index = UNTAR_BOWTIE2_INDEX([[:], bowtie2_index]).untar
185-
ch_versions = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
186-
}
187-
else {
169+
ch_versions = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
170+
} else {
188171
ch_bowtie2_index = [[:], file(bowtie2_index)]
189172
}
190-
}
191-
else {
173+
} else {
192174
ch_bowtie2_index = BOWTIE2_BUILD(ch_fasta.map { [[:], it] }).index
193-
ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions)
175+
ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions)
194176
}
195177
}
196178

@@ -202,15 +184,13 @@ workflow PREPARE_GENOME {
202184
if (chromap_index) {
203185
if (chromap_index.endsWith('.tar.gz')) {
204186
ch_chromap_index = UNTARFILES([[:], chromap_index]).files
205-
ch_versions = ch_versions.mix(UNTARFILES.out.versions)
206-
}
207-
else {
187+
ch_versions = ch_versions.mix(UNTARFILES.out.versions)
188+
} else {
208189
ch_chromap_index = [[:], file(chromap_index)]
209190
}
210-
}
211-
else {
191+
} else {
212192
ch_chromap_index = CHROMAP_INDEX(ch_fasta.map { [[:], it] }).index
213-
ch_versions = ch_versions.mix(CHROMAP_INDEX.out.versions)
193+
ch_versions = ch_versions.mix(CHROMAP_INDEX.out.versions)
214194
}
215195
}
216196

@@ -222,28 +202,26 @@ workflow PREPARE_GENOME {
222202
if (star_index) {
223203
if (star_index.endsWith('.tar.gz')) {
224204
ch_star_index = UNTAR_STAR_INDEX([[:], star_index]).untar.map { it[1] }
225-
ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
226-
}
227-
else {
205+
ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
206+
} else {
228207
ch_star_index = Channel.value(file(star_index))
229208
}
230-
}
231-
else {
209+
} else {
232210
ch_star_index = STAR_GENOMEGENERATE(ch_fasta, ch_gtf).index
233-
ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
211+
ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
234212
}
235213
}
236214

237215
emit:
238-
fasta = ch_fasta // path: genome.fasta
239-
fai = ch_fai // path: genome.fai
240-
gtf = ch_gtf // path: genome.gtf
241-
gene_bed = ch_gene_bed // path: gene.bed
242-
chrom_sizes = ch_chrom_sizes // path: genome.sizes
243-
filtered_bed = ch_genome_filtered_bed // path: *.include_regions.bed
244-
bwa_index = ch_bwa_index // path: bwa/index/
245-
bowtie2_index = ch_bowtie2_index // path: bowtie2/index/
246-
chromap_index = ch_chromap_index // path: genome.index
247-
star_index = ch_star_index // path: star/index/
216+
fasta = ch_fasta // path: genome.fasta
217+
fai = ch_fai // path: genome.fai
218+
gtf = ch_gtf // path: genome.gtf
219+
gene_bed = ch_gene_bed // path: gene.bed
220+
chrom_sizes = ch_chrom_sizes // path: genome.sizes
221+
filtered_bed = ch_genome_filtered_bed // path: *.include_regions.bed
222+
bwa_index = ch_bwa_index // path: bwa/index/
223+
bowtie2_index = ch_bowtie2_index // path: bowtie2/index/
224+
chromap_index = ch_chromap_index // path: genome.index
225+
star_index = ch_star_index // path: star/index/
248226
versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
249227
}

0 commit comments

Comments
 (0)