Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Dp24 only csi #259

Merged
merged 1 commit into from
Feb 16, 2024
Merged

Dp24 only csi #259

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 4 additions & 3 deletions conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -170,7 +170,8 @@ process {

withName: ".*:.*:GAP_FINDER:TABIX_BGZIPTABIX" {
ext.prefix = { "gap_${meta.id}" }
ext.args2 = { "${meta.max_scaff >= 500000000 ? "--csi" : "" }" }
ext.args = ""
ext.args2 = { "--csi" }
}


Expand All @@ -196,7 +197,7 @@ process {

withName: ".*:.*:.*:PEP_ALIGNMENTS:TABIX_BGZIPTABIX" {
ext.prefix = { "pep_${meta.id}" }
ext.args2 = { "${meta.max_scaff >= 500000000 ? "--csi" : "" }" }
ext.args2 = { "--csi" }
}

//
Expand Down Expand Up @@ -293,7 +294,7 @@ process {

withName: ".*:.*:TELO_FINDER:TABIX_BGZIPTABIX" {
ext.prefix = { "telo_${meta.id}" }
ext.args2 = { "${meta.max_scaff >= 500000000 ? "--csi" : "" }" }
ext.args2 = { "--csi" }

}

Expand Down
16 changes: 1 addition & 15 deletions subworkflows/local/gap_finder.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main'
workflow GAP_FINDER {
take:
reference_tuple // Channel: tuple [ val(meta), path(fasta) ]
max_scaff_size // Channel: val(size of largest scaffold in bp)

main:
ch_versions = Channel.empty()
Expand All @@ -31,24 +30,11 @@ workflow GAP_FINDER {
)
ch_versions = ch_versions.mix( GAP_LENGTH.out.versions )

//
// LOGIC: Adding the largest scaffold size to the meta data so it can be used in the modules.config
//
SEQTK_CUTN.out.bed
.combine(max_scaff_size)
.map {meta, row, scaff ->
tuple([ id : meta.id,
max_scaff : scaff
],
file(row)
)}
.set { modified_bed_ch }

//
// MODULE: BGZIP AND TABIX THE GAP FILE
//
TABIX_BGZIPTABIX (
modified_bed_ch
SEQTK_CUTN.out.bed
)
ch_versions = ch_versions.mix( TABIX_BGZIPTABIX.out.versions )

Expand Down
2 changes: 0 additions & 2 deletions subworkflows/local/gene_alignment.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ workflow GENE_ALIGNMENT {
dot_genome // Channel: [ val(meta), path(file) ]
reference_tuple // Channel: [ val(meta), path(file) ]
reference_index // Channel: [ val(meta), path(file) ]
max_scaff_size // Channel: val(size of largest scaffold in bp)
alignment_datadir // Channel: val(geneset_dir)
alignment_genesets // Channel: val(geneset_id)
alignment_common // Channel: val(common_name) // Not yet in use
Expand Down Expand Up @@ -83,7 +82,6 @@ workflow GENE_ALIGNMENT {
//
PEP_ALIGNMENTS ( reference_tuple,
pep_files,
max_scaff_size
)
ch_versions = ch_versions.mix(PEP_ALIGNMENTS.out.versions)

Expand Down
14 changes: 1 addition & 13 deletions subworkflows/local/pep_alignments.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,6 @@ workflow PEP_ALIGNMENTS {
take:
reference_tuple // Channel: tuple [ val(meta), path(file) ]
pep_files // Channel: tuple [ val(meta), path(file) ]
max_scaff_size // Channel: tuple val(size of largest scaffold in bp)

main:
ch_versions = Channel.empty()
Expand Down Expand Up @@ -109,23 +108,12 @@ workflow PEP_ALIGNMENTS {
)
ch_versions = ch_versions.mix( EXTRACT_COV_IDEN.out.versions )

BEDTOOLS_SORT.out.sorted
.combine( max_scaff_size )
.map {meta, row, scaff ->
tuple(
[ id : meta.id,
max_scaff : scaff >= 500000000 ? 'csi': '' ],
file( row )
)
}
.set { modified_bed_ch }

//
// MODULE: COMPRESS AND INDEX MERGED.GFF
// EMITS A TBI FILE
//
TABIX_BGZIPTABIX (
modified_bed_ch
BEDTOOLS_SORT.out.sorted
)
ch_versions = ch_versions.mix( TABIX_BGZIPTABIX.out.versions )

Expand Down
17 changes: 1 addition & 16 deletions subworkflows/local/telo_finder.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,6 @@ include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptab
workflow TELO_FINDER {

take:
max_scaff_size // Channel: val(size of largest scaffold in bp)
reference_tuple // Channel: tuple [ val(meta), path(fasta) ]
teloseq

Expand Down Expand Up @@ -43,25 +42,11 @@ workflow TELO_FINDER {
)
ch_versions = ch_versions.mix( EXTRACT_TELO.out.versions )

//
// LOGIC: Adding the largest scaffold size to the meta data so it can be used in the modules.config
//
EXTRACT_TELO.out.bed
.combine(max_scaff_size)
.map {meta, row, scaff ->
tuple(
[ id : meta.id,
max_scaff : scaff ],
file( row )
)
}
.set { modified_bed_ch }

//
// MODULE: BGZIP AND TABIX THE OUTPUT FILE
//
TABIX_BGZIPTABIX (
modified_bed_ch
EXTRACT_TELO.out.bed
)
ch_versions = ch_versions.mix( TABIX_BGZIPTABIX.out.versions )

Expand Down
5 changes: 1 addition & 4 deletions workflows/treeval.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,6 @@ workflow TREEVAL {
GENERATE_GENOME.out.dot_genome,
YAML_INPUT.out.reference_ch,
GENERATE_GENOME.out.ref_index,
GENERATE_GENOME.out.max_scaff_size,
YAML_INPUT.out.align_data_dir,
YAML_INPUT.out.align_geneset,
YAML_INPUT.out.align_common,
Expand All @@ -162,7 +161,6 @@ workflow TREEVAL {
//
GAP_FINDER (
YAML_INPUT.out.reference_ch,
GENERATE_GENOME.out.max_scaff_size
)
ch_versions = ch_versions.mix( GAP_FINDER.out.versions )

Expand Down Expand Up @@ -202,8 +200,7 @@ workflow TREEVAL {
//
// SUBWORKFLOW: GENERATE TELOMERE WINDOW FILES WITH PACBIO READS AND REFERENCE
//
TELO_FINDER ( GENERATE_GENOME.out.max_scaff_size,
YAML_INPUT.out.reference_ch,
TELO_FINDER ( YAML_INPUT.out.reference_ch,
YAML_INPUT.out.teloseq
)
ch_versions = ch_versions.mix( TELO_FINDER.out.versions )
Expand Down
Loading