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

Add CHM13 igenomes reference #64

Merged
merged 8 commits into from
Sep 22, 2022
Merged

Add CHM13 igenomes reference #64

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
f05984d
feat(CHM13): Add references
edmundmiller Aug 23, 2022
76cf06d
fix(alignment): Update bwamem2 index
edmundmiller Aug 23, 2022
2d97914
fix(CHM13): Use FTP links for now
edmundmiller Aug 24, 2022
b7688a5
fix(CHM13): Use fasta with chrNames
edmundmiller Sep 2, 2022
2f2f7e6
feat(CHM13): Add igenomes s3 refs
edmundmiller Sep 12, 2022
d4d8d93
feat(CHM13): Add mito chrom name
edmundmiller Sep 17, 2022
d5ab5d3
chore: Add bwamem2 index to schema
edmundmiller Sep 19, 2022
f52ac20
chore: Update CHANGELOG
edmundmiller Sep 19, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- [[#28](https://github.com/nf-core/nascent/issues/28)] - Added DRAGMAP alignment
- [[#64](https://github.com/nf-core/nascent/pull/64)] - Added CHM13 igenomes config

### `Fixed`

Expand Down
8 changes: 8 additions & 0 deletions conf/igenomes.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,14 @@ params {
macs_gsize = "2.7e9"
blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
}
'CHM13' {
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
mito_name = "chrM"
}
'GRCm38' {
fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
Expand Down
1 change: 1 addition & 0 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
params.gff = WorkflowMain.getGenomeAttribute(params, 'gff')
params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'bed12')
params.bwa_index = WorkflowMain.getGenomeAttribute(params, 'bwa')
params.bwamem2_index = WorkflowMain.getGenomeAttribute(params, 'bwamem2')
params.dragmap = WorkflowMain.getGenomeAttribute(params, 'dragmap')

/*
Expand Down
7 changes: 7 additions & 0 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,13 @@
"fa_icon": "fas fa-copy",
"help_text": "> **NB** If none provided, will be generated automatically from the FASTA reference."
},
"bwamem2_index": {
"type": "string",
"description": "Path to bwa-mem2 mem indices.",
"fa_icon": "fas fa-copy",
"help_text": "> **NB** If none provided, will be generated automatically from the FASTA reference.",
"hidden": true
},
"dragmap": {
"type": "string",
"fa_icon": "fas fa-copy",
Expand Down
8 changes: 4 additions & 4 deletions subworkflows/local/prepare_genome.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,11 +95,11 @@ workflow PREPARE_GENOME {
ch_versions = ch_versions.mix(BWA_INDEX.out.versions)
}
} else if ('bwamem2' in prepare_tool_indices) {
if (params.bwa_index) {
if (params.bwa_index.endsWith('.tar.gz')) {
ch_bwa_index = UNTAR_BWA_INDEX ( params.bwa_index ).untar
if (params.bwamem2_index) {
if (params.bwamem2_index.endsWith('.tar.gz') || params.bwamem2_index.endsWith('.tgz')) {
ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], params.bwamem2_index ] ).untar
} else {
ch_bwa_index = file(params.bwa_index)
ch_bwa_index = file(params.bwamem2_index)
}
} else {
ch_bwa_index = BWAMEM2_INDEX ( ch_fasta ).index
Expand Down