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Rename bwa-mem2 index variables #34

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May 17, 2024
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Rename bwa-mem2 index variables #34

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f1fe44d
Rename bwa-mem2 index variables
scwatts May 16, 2024
5ea55f5
Use correct bwa-mem2 pointers in usage.md
scwatts May 17, 2024
112d239
Correct typo usage.md
scwatts May 17, 2024
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24 changes: 12 additions & 12 deletions conf/hmf_genomes.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,20 +10,20 @@
params {
genomes {
'GRCh37_hmf' {
fasta = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/Homo_sapiens.GRCh37.GATK.illumina.fasta"
fai = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.fai"
dict = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.dict"
bwa_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/bwa_index/2.2.1.tar.gz"
gridss_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/gridss_index/2.13.2.tar.gz"
star_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/star_index/gencode_19/2.7.3a.tar.gz"
fasta = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/Homo_sapiens.GRCh37.GATK.illumina.fasta"
fai = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.fai"
dict = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.dict"
bwamem2_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz"
gridss_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/gridss_index/2.13.2.tar.gz"
star_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/star_index/gencode_19/2.7.3a.tar.gz"
}
'GRCh38_hmf' {
fasta = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
fai = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai"
dict = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict"
bwa_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/bwa_index/2.2.1.tar.gz"
gridss_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/gridss_index/2.13.2.tar.gz"
star_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/star_index/gencode_38/2.7.3a.tar.gz"
fasta = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
fai = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai"
dict = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict"
bwamem2_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz"
gridss_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/gridss_index/2.13.2.tar.gz"
star_index = "https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/star_index/gencode_38/2.7.3a.tar.gz"
}
}
}
12 changes: 6 additions & 6 deletions conf/test_stub.config
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Expand Up @@ -26,12 +26,12 @@ params {
genomes {

'GRCh38_hmf' {
fasta = "temp/GRCh38.fasta"
fai = "temp/GRCh38.fai"
dict = "temp/GRCh38.dict"
bwa_index = "temp/GRCh38_bwa-mem2_index/"
gridss_index = "temp/GRCh38_gridss_index/"
star_index = "temp/GRCh38_star_index/"
fasta = "temp/GRCh38.fasta"
fai = "temp/GRCh38.fai"
dict = "temp/GRCh38.dict"
bwamem2_index = "temp/GRCh38_bwa-mem2_index/"
gridss_index = "temp/GRCh38_gridss_index/"
star_index = "temp/GRCh38_star_index/"
}

}
Expand Down
6 changes: 3 additions & 3 deletions docs/usage.md
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Expand Up @@ -334,7 +334,7 @@ params {
fasta = "/path/to/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
fai = "/path/to/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai"
dict = "/path/to/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict"
bwa_index = "/path/to/bwa-mem2_index/"
bwamem2_index = "/path/to/bwa-mem2_index/"
gridss_index = "/path/to/gridss_index/"
star_index = "/path/to/star_index/"
}
Expand All @@ -357,7 +357,7 @@ _GRCh37 genome (Hartwig) [`GRCh37_hmf`]_
| FASTA | [Homo_sapiens.GRCh37.GATK.illumina.fasta](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/Homo_sapiens.GRCh37.GATK.illumina.fasta) |
| FASTA index | [Homo_sapiens.GRCh37.GATK.illumina.fasta.fai](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.fai) |
| FASTA seq dictionary | [Homo_sapiens.GRCh37.GATK.illumina.fasta.dict](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/samtools_index/1.16/Homo_sapiens.GRCh37.GATK.illumina.fasta.dict) |
| bwa-mem2 index | [bwa_index/2.2.1.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/bwa_index/2.2.1.tar.gz) |
| bwa-mem2 index | [bwa-mem2_index/2.2.1.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz) |
| GRIDSS index | [gridss_index/2.13.2.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.1/gridss_index/2.13.2.tar.gz) |
| STAR index | [star_index/gencode_19/2.7.3a.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh37_hmf/24.0/star_index/gencode_19/2.7.3a.tar.gz) |

Expand All @@ -368,7 +368,7 @@ _GRCh38 genome (Hartwig) [`GRCh38_hmf`]_
| FASTA | [GCA_000001405.15_GRCh38_no_alt_analysis_set.fna](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna) |
| FASTA index | [GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai) |
| FASTA seq dictionary | [GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/samtools_index/1.16/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict) |
| bwa-mem2 index | [bwa_index/2.2.1.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/bwa_index/2.2.1.tar.gz) |
| bwa-mem2 index | [bwa-mem2_index/2.2.1.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/bwa-mem2_index/2.2.1.tar.gz) |
| GRIDSS index | [gridss_index/2.13.2.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/gridss_index/2.13.2.tar.gz) |
| STAR index | [star_index/gencode_38/2.7.3a.tar.gz](https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/star_index/gencode_38/2.7.3a.tar.gz) |

Expand Down
5 changes: 3 additions & 2 deletions lib/Utils.groovy
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Expand Up @@ -197,12 +197,13 @@ class Utils {

def fps = [
params.ref_data_genome_alt,
params.ref_data_genome_bwa_index,
params.ref_data_genome_bwamem2_index,
params.ref_data_genome_dict,
params.ref_data_genome_fai,
params.ref_data_genome_fasta,
params.ref_data_genome_gridss_index,
params.ref_data_genome_gtf,
params.ref_data_genome_star_index,
params.ref_data_virusbreakenddb_path,
]

Expand Down Expand Up @@ -323,7 +324,7 @@ class Utils {
def has_alt_contigs = params.genome_type == 'alt'

// Ensure that custom genomes with ALT contigs that need indexes built have the required .alt file
def has_bwa_indexes = (params.ref_data_genome_bwa_index && params.ref_data_genome_gridss_index)
def has_bwa_indexes = (params.ref_data_genome_bwamem2_index && params.ref_data_genome_gridss_index)
def has_alt_file = params.containsKey('ref_data_genome_alt') && params.ref_data_genome_alt
def run_bwa_or_gridss_index = run_config.stages.alignment && run_config.has_dna_fastq && !has_bwa_indexes

Expand Down
12 changes: 6 additions & 6 deletions main.nf
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Expand Up @@ -31,12 +31,12 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_oncoanaly
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

params.ref_data_genome_fasta = getGenomeAttribute('fasta')
params.ref_data_genome_fai = getGenomeAttribute('fai')
params.ref_data_genome_dict = getGenomeAttribute('dict')
params.ref_data_genome_bwa_index = getGenomeAttribute('bwa_index')
params.ref_data_genome_gridss_index = getGenomeAttribute('gridss_index')
params.ref_data_genome_star_index = getGenomeAttribute('star_index')
params.ref_data_genome_fasta = getGenomeAttribute('fasta')
params.ref_data_genome_fai = getGenomeAttribute('fai')
params.ref_data_genome_dict = getGenomeAttribute('dict')
params.ref_data_genome_bwamem2_index = getGenomeAttribute('bwamem2_index')
params.ref_data_genome_gridss_index = getGenomeAttribute('gridss_index')
params.ref_data_genome_star_index = getGenomeAttribute('star_index')

WorkflowMain.setParamsDefaults(params, log)
WorkflowMain.validateParams(params, log)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/bwa-mem2/mem/main.nf
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Expand Up @@ -10,7 +10,7 @@ process BWAMEM2_ALIGN {
input:
tuple val(meta), path(reads_fwd), path(reads_rev)
path genome_fasta
path genome_bwa_index
path genome_bwamem2_index

output:
tuple val(meta), path('*.bam'), path('*.bai'), emit: bam
Expand All @@ -28,7 +28,7 @@ process BWAMEM2_ALIGN {
def output_fn = meta.split ? "${meta.split}.${meta.sample_id}.${meta.read_group}.bam" : "${meta.sample_id}.${meta.read_group}.bam"

"""
ln -fs \$(find -L ${genome_bwa_index} -type f) ./
ln -fs \$(find -L ${genome_bwamem2_index} -type f) ./

bwa-mem2 mem \\
${args} \\
Expand Down
4 changes: 2 additions & 2 deletions modules/local/bwa-mem2/mem/meta.yml
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Expand Up @@ -29,9 +29,9 @@ input:
type: file
description: Reference genome assembly FASTA file
pattern: "*.{fa,fasta}"
- genome_bwa_index:
- genome_bwamem2_index:
type: directory
description: bwa-mem1 index directory
description: bwa-mem2 index directory
output:
- meta:
type: map
Expand Down
2 changes: 1 addition & 1 deletion modules/local/custom/lilac_extract_and_index_contig/main.nf
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Expand Up @@ -15,7 +15,7 @@ process CUSTOM_EXTRACTCONTIG {

output:
path "*extracted.fa" , emit: contig
path "*extracted.fa.*", emit: bwa_index
path "*extracted.fa.*", emit: bwamem2_index
path 'versions.yml' , emit: versions

when:
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -78,7 +78,7 @@ params {
'panel_data_paths',
'ref_data',
'ref_data_genome_alt',
'ref_data_genome_bwa_index',
'ref_data_genome_bwamem2_index',
'ref_data_genome_dict',
'ref_data_genome_fai',
'ref_data_genome_fasta',
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/lilac_calling/main.nf
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Expand Up @@ -131,7 +131,7 @@ workflow LILAC_CALLING {
REALIGNREADS(
SLICEBAM.out.bam,
EXTRACTCONTIG.out.contig,
EXTRACTCONTIG.out.bwa_index,
EXTRACTCONTIG.out.bwamem2_index,
)

ch_versions = ch_versions.mix(REALIGNREADS.out.versions)
Expand Down
44 changes: 22 additions & 22 deletions subworkflows/local/prepare_reference/main.nf
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Expand Up @@ -55,28 +55,28 @@ workflow PREPARE_REFERENCE {
//
// Set bwa-mem2 index, unpack or create if required
//
ch_genome_bwa_index = Channel.empty()
ch_genome_bwamem2_index = Channel.empty()
if (run_config.has_dna && run_config.stages.alignment) {
if (!params.ref_data_genome_bwa_index) {
if (!params.ref_data_genome_bwamem2_index) {

BWAMEM2_INDEX(
ch_genome_fasta,
params.ref_data_genome_alt ? file(params.ref_data_genome_alt) : [],
)
ch_genome_bwa_index = BWAMEM2_INDEX.out.index
ch_genome_bwamem2_index = BWAMEM2_INDEX.out.index
ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)

} else if (params.ref_data_genome_bwa_index.endsWith('.tar.gz')) {
} else if (params.ref_data_genome_bwamem2_index.endsWith('.tar.gz')) {

ch_genome_bwa_index_inputs = Channel.fromPath(params.ref_data_genome_bwa_index)
ch_genome_bwamem2_index_inputs = Channel.fromPath(params.ref_data_genome_bwamem2_index)
.map { [[id: "bwa-mem2_index_${it.name.replaceAll('\\.tar\\.gz$', '')}"], it] }

DECOMP_BWAMEM2_INDEX(ch_genome_bwa_index_inputs)
ch_genome_bwa_index = DECOMP_BWAMEM2_INDEX.out.dir
DECOMP_BWAMEM2_INDEX(ch_genome_bwamem2_index_inputs)
ch_genome_bwamem2_index = DECOMP_BWAMEM2_INDEX.out.dir

} else {

ch_genome_bwa_index = getRefFileChannel('ref_data_genome_bwa_index')
ch_genome_bwamem2_index = getRefFileChannel('ref_data_genome_bwamem2_index')

}
}
Expand Down Expand Up @@ -235,7 +235,7 @@ workflow PREPARE_REFERENCE {
ch_genome_fasta,
ch_genome_fai,
ch_genome_dict,
ch_genome_bwa_index,
ch_genome_bwamem2_index,
ch_genome_gridss_index,
ch_genome_star_index,
ch_virusbreakenddb,
Expand All @@ -258,19 +258,19 @@ workflow PREPARE_REFERENCE {
}

emit:
genome_fasta = ch_genome_fasta.first() // path: genome_fasta
genome_fai = ch_genome_fai.first() // path: genome_fai
genome_dict = ch_genome_dict.first() // path: genome_dict
genome_bwa_index = ch_genome_bwa_index.first() // path: genome_bwa_index
genome_gridss_index = ch_genome_gridss_index.first() // path: genome_gridss_index
genome_star_index = ch_genome_star_index.first() // path: genome_star_index
genome_version = ch_genome_version // val: genome_version

virusbreakenddb = ch_virusbreakenddb.first() // path: VIRUSBreakend database
hmf_data = ch_hmf_data // map: HMF data paths
panel_data = ch_panel_data // map: Panel data paths

versions = ch_versions // channel: [ versions.yml ]
genome_fasta = ch_genome_fasta.first() // path: genome_fasta
genome_fai = ch_genome_fai.first() // path: genome_fai
genome_dict = ch_genome_dict.first() // path: genome_dict
genome_bwamem2_index = ch_genome_bwamem2_index.first() // path: genome_bwa-mem2_index
genome_gridss_index = ch_genome_gridss_index.first() // path: genome_gridss_index
genome_star_index = ch_genome_star_index.first() // path: genome_star_index
genome_version = ch_genome_version // val: genome_version

virusbreakenddb = ch_virusbreakenddb.first() // path: VIRUSBreakend database
hmf_data = ch_hmf_data // map: HMF data paths
panel_data = ch_panel_data // map: Panel data paths

versions = ch_versions // channel: [ versions.yml ]
}

def getRefFileChannel(key) {
Expand Down
28 changes: 14 additions & 14 deletions subworkflows/local/read_alignment_dna/main.nf
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Expand Up @@ -15,7 +15,7 @@ workflow READ_ALIGNMENT_DNA {

// Reference data
genome_fasta // channel: [mandatory] /path/to/genome_fasta
genome_bwa_index // channel: [mandatory] /path/to/genome_bwa_index_dir/
genome_bwamem2_index // channel: [mandatory] /path/to/genome_bwa-mem2_index_dir/

// Params
max_fastq_records // numeric: [mandatory] max number of FASTQ records per split
Expand Down Expand Up @@ -128,11 +128,11 @@ workflow READ_ALIGNMENT_DNA {
// MODULE: BWA-MEM2
//
// Create process input channel
// channel: [ meta_bwa, fastq_fwd, fastq_rev ]
ch_bwa_inputs = ch_fastqs_ready
// channel: [ meta_bwamem2, fastq_fwd, fastq_rev ]
ch_bwamem2_inputs = ch_fastqs_ready
.map { meta_fastq_ready, fastq_fwd, fastq_rev ->

def meta_bwa = [
def meta_bwamem2 = [
*:meta_fastq_ready,


Expand All @@ -142,40 +142,40 @@ workflow READ_ALIGNMENT_DNA {

]

return [meta_bwa, fastq_fwd, fastq_rev]
return [meta_bwamem2, fastq_fwd, fastq_rev]
}

// Run process
BWAMEM2_ALIGN(
ch_bwa_inputs,
ch_bwamem2_inputs,
genome_fasta,
genome_bwa_index,
genome_bwamem2_index,
)

ch_versions = ch_versions.mix(BWAMEM2_ALIGN.out.versions)

// Reunite BAMs
// First, count expected BAMs per sample for non-blocking groupTuple op
// channel: [ meta_count, group_size ]
ch_sample_fastq_counts = ch_bwa_inputs
.map { meta_bwa, reads_fwd, reads_rev ->
ch_sample_fastq_counts = ch_bwamem2_inputs
.map { meta_bwamem2, reads_fwd, reads_rev ->

def meta_count = [
key: meta_bwa.key,
sample_type: meta_bwa.sample_type,
key: meta_bwamem2.key,
sample_type: meta_bwamem2.sample_type,
]

return [meta_count, meta_bwa]
return [meta_count, meta_bwamem2]
}
.groupTuple()
.map { meta_count, meta_bwas -> return [meta_count, meta_bwas.size()] }
.map { meta_count, metas_bwamem2 -> return [meta_count, metas_bwamem2.size()] }

// Now, group with expected size then sort into tumor and normal channels
// channel: [ meta_group, [bam, ...], [bai, ...] ]
ch_bams_united = ch_sample_fastq_counts
.cross(
// First element to match meta_count above for `cross`
BWAMEM2_ALIGN.out.bam.map { meta_bwa, bam, bai -> [[key: meta_bwa.key, sample_type: meta_bwa.sample_type], bam, bai] }
BWAMEM2_ALIGN.out.bam.map { meta_bwamem2, bam, bai -> [[key: meta_bwamem2.key, sample_type: meta_bwamem2.sample_type], bam, bai] }
)
.map { count_tuple, bam_tuple ->

Expand Down
2 changes: 1 addition & 1 deletion workflows/targeted.nf
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Expand Up @@ -114,7 +114,7 @@ workflow TARGETED {
READ_ALIGNMENT_DNA(
ch_inputs,
ref_data.genome_fasta,
ref_data.genome_bwa_index,
ref_data.genome_bwamem2_index,
params.max_fastq_records,
)

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2 changes: 1 addition & 1 deletion workflows/wgts.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ workflow WGTS {
READ_ALIGNMENT_DNA(
ch_inputs,
ref_data.genome_fasta,
ref_data.genome_bwa_index,
ref_data.genome_bwamem2_index,
params.max_fastq_records,
)

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