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Parabricks alignment #1444

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Parabricks alignment #1444

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a5e71ec
installed fq2bam
Furentsu Feb 13, 2024
6652f01
included fq2bam module
Furentsu Feb 29, 2024
0b3a6f0
started fastq2bam integration into alignment subworkflow
Furentsu Mar 1, 2024
5158657
added parabricks fq2bam to fast_align_bwamem_mem2_dragmap_sentieon su…
Furentsu Mar 9, 2024
b1ca9ed
integration of fq2bam - WIP
Furentsu Mar 18, 2024
bd1981e
draft pr
Furentsu Mar 20, 2024
881bd34
Merge branch 'dev' into parabricks_alignment
maxulysse Apr 11, 2024
3c05085
fix channel input
maxulysse Apr 11, 2024
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5 changes: 5 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -339,6 +339,11 @@
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["bam_ngscheckmate"]
},
"parabricks/fq2bam": {
"branch": "master",
"git_sha": "2fe1d9713a234768540b9fb0ee515e52dc613ddf",
"installed_by": ["modules"]
},
"samblaster": {
"branch": "master",
"git_sha": "310850152f3e1dec6ba28b28e1f1cb9ab8660a49",
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90 changes: 90 additions & 0 deletions modules/nf-core/parabricks/fq2bam/main.nf
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83 changes: 83 additions & 0 deletions modules/nf-core/parabricks/fq2bam/meta.yml
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18 changes: 17 additions & 1 deletion subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf
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Expand Up @@ -8,17 +8,19 @@ include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/ma
include { BWA_MEM as BWAMEM1_MEM } from '../../../modules/nf-core/bwa/mem/main'
include { DRAGMAP_ALIGN } from '../../../modules/nf-core/dragmap/align/main'
include { SENTIEON_BWAMEM } from '../../../modules/nf-core/sentieon/bwamem/main'
include { PARABRICKS_FQ2BAM } from '../../../modules/nf-core/parabricks/fq2bam/main'

workflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON {
take:
reads // channel: [mandatory] meta, reads
// interval_file // channel: [optional for parabricks] intervals_bed_combined
index // channel: [mandatory] index
sort // boolean: [mandatory] true -> sort, false -> don't sort
fasta
fasta_fai
// known_sites // channel [optional for parabricks] known_sites_indels

main:

versions = Channel.empty()
reports = Channel.empty()

Expand All @@ -28,6 +30,9 @@ workflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON {
DRAGMAP_ALIGN(reads, index, [[id:'no_fasta'], []], sort) // If aligner is dragmap
// The sentieon-bwamem-module does sorting as part of the conversion from sam to bam.
SENTIEON_BWAMEM(reads, index, fasta, fasta_fai) // If aligner is sentieon-bwamem
// The parabricks-fq2bam module performs alignment and sorting as part of the conversion from fastq to bam.
// Additionally, it can perform mark duplicates and generate a bqsr table (input for parabricks-applybqsr module)
PARABRICKS_FQ2BAM(reads.map{meta, reads -> [meta, reads, []] } , fasta, index, [])

// Get the bam files from the aligner
// Only one aligner is run
Expand All @@ -36,8 +41,15 @@ workflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON {
bam = bam.mix(BWAMEM2_MEM.out.bam)
bam = bam.mix(DRAGMAP_ALIGN.out.bam)
bam = bam.mix(SENTIEON_BWAMEM.out.bam_and_bai.map{ meta, bam, bai -> [ meta, bam ] })
bam = bam.mix(PARABRICKS_FQ2BAM.out.bam)

bai = SENTIEON_BWAMEM.out.bam_and_bai.map{ meta, bam, bai -> [ meta, bai ] }
bai = bai.mix(PARABRICKS_FQ2BAM.out.bai)

// Optional outputs for parabricks_fq2bam
qc_metrics = PARABRICKS_FQ2BAM.out.qc_metrics
bqsr_table = PARABRICKS_FQ2BAM.out.bqsr_table
duplicate_metrics = PARABRICKS_FQ2BAM.out.duplicate_metrics

// Gather reports of all tools used
reports = reports.mix(DRAGMAP_ALIGN.out.log)
Expand All @@ -47,10 +59,14 @@ workflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON {
versions = versions.mix(BWAMEM2_MEM.out.versions)
versions = versions.mix(DRAGMAP_ALIGN.out.versions)
versions = versions.mix(SENTIEON_BWAMEM.out.versions)
versions = versions.mix(PARABRICKS_FQ2BAM.out.versions)

emit:
bam // channel: [ [meta], bam ]
bai // channel: [ [meta], bai ]
qc_metrics // file: qc_metrics/alignment.txt
bqsr_table // file: *.table
duplicate_metrics // file: duplicate-metrics.txt
reports
versions // channel: [ versions.yml ]
}
6 changes: 3 additions & 3 deletions workflows/sarek/main.nf
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Expand Up @@ -324,7 +324,7 @@ workflow SAREK {
versions = versions.mix(FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON.out.versions)
}

if (params.step in ['mapping', 'markduplicates']) {
if (params.step in ['mapping', 'markduplicates'] && !params.step in ['parabricks']) {

// ch_cram_no_markduplicates_restart = Channel.empty()
cram_markduplicates_no_spark = Channel.empty()
Expand Down Expand Up @@ -437,7 +437,7 @@ workflow SAREK {
else CHANNEL_MARKDUPLICATES_CREATE_CSV(ch_md_cram_for_restart, csv_subfolder, params.outdir, params.save_output_as_bam)
}

if (params.step in ['mapping', 'markduplicates', 'prepare_recalibration']) {
if (params.step in ['mapping', 'markduplicates', 'prepare_recalibration'] && !params.step in ['parabricks']) {

// Run if starting from step "prepare_recalibration"
if (params.step == 'prepare_recalibration') {
Expand Down Expand Up @@ -473,7 +473,7 @@ workflow SAREK {
}

// STEP 3: Create recalibration tables
if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')) && !params.step in ['parabricks']) {

ch_table_bqsr_no_spark = Channel.empty()
ch_table_bqsr_spark = Channel.empty()
Expand Down
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