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Installing and calling nf-core/modules version of sentieon/bwamem #398

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merged 2 commits into from
Aug 9, 2023
Merged

Installing and calling nf-core/modules version of sentieon/bwamem #398

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90e1861
Installing and calling nf-core/modules version of sentieon/bwamem
asp8200 Aug 9, 2023
78eaee6
Moving setup of sentieon-secrets to test.config
asp8200 Aug 9, 2023
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1 change: 1 addition & 0 deletions conf/modules/align_sentieon.config
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
//

process {

withName: '.*ALIGN_SENTIEON:.*' {
ext.when = params.aligner.equals("sentieon")
}
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7 changes: 7 additions & 0 deletions conf/test.config
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Expand Up @@ -50,3 +50,10 @@ params {
vep_filters = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
vep_cache_version = 107
}

process {
withLabel: 'sentieon' {
ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
}
}
5 changes: 5 additions & 0 deletions modules.json
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Expand Up @@ -345,6 +345,11 @@
"git_sha": "49af8ed458e28729e483bc96e5a57c28163b9ea0",
"installed_by": ["modules"]
},
"sentieon/bwamem": {
"branch": "master",
"git_sha": "b9172e8c26a3db5009f7872654c44587e254f094",
"installed_by": ["modules"]
},
"smncopynumbercaller": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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68 changes: 0 additions & 68 deletions modules/local/sentieon/bwamem.nf
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78 changes: 78 additions & 0 deletions modules/nf-core/sentieon/bwamem/main.nf
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63 changes: 63 additions & 0 deletions modules/nf-core/sentieon/bwamem/meta.yml
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7 changes: 3 additions & 4 deletions subworkflows/local/alignment/align_sentieon.nf
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Expand Up @@ -2,7 +2,7 @@
// A subworkflow to annotate structural variants.
//

include { SENTIEON_BWAMEM } from '../../../modules/local/sentieon/bwamem'
include { SENTIEON_BWAMEM } from '../../../modules/nf-core/sentieon/bwamem/main'
include { SENTIEON_DATAMETRICS } from '../../../modules/local/sentieon/datametrics'
include { SENTIEON_LOCUSCOLLECTOR } from '../../../modules/local/sentieon/locuscollector'
include { SENTIEON_DEDUP } from '../../../modules/local/sentieon/dedup'
Expand All @@ -25,11 +25,10 @@ workflow ALIGN_SENTIEON {
ch_bqsr_bai = Channel.empty()
ch_bqsr_csv = Channel.empty()

SENTIEON_BWAMEM ( ch_reads_input, ch_genome_fasta, ch_genome_fai, ch_bwa_index )
SENTIEON_BWAMEM ( ch_reads_input, ch_bwa_index, ch_genome_fasta.map{ meta, fasta -> fasta }, ch_genome_fai.map{ meta, fai -> fai })

SENTIEON_BWAMEM.out
.bam
.join(SENTIEON_BWAMEM.out.bai, failOnMismatch:true, failOnDuplicate:true)
.bam_and_bai
.map{ meta, bam, bai ->
new_id = meta.id.split('_')[0]
new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"]
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6 changes: 3 additions & 3 deletions subworkflows/local/mitochondria/align_and_call_MT.nf
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Expand Up @@ -2,7 +2,7 @@
// Align and call MT
//

include { SENTIEON_BWAMEM as SENTIEON_BWAMEM_MT } from '../../../modules/local/sentieon/bwamem'
include { SENTIEON_BWAMEM as SENTIEON_BWAMEM_MT } from '../../../modules/nf-core/sentieon/bwamem/main'
include { BWAMEM2_MEM as BWAMEM2_MEM_MT } from '../../../modules/nf-core/bwamem2/mem/main'
include { GATK4_MERGEBAMALIGNMENT as GATK4_MERGEBAMALIGNMENT_MT } from '../../../modules/nf-core/gatk4/mergebamalignment/main'
include { PICARD_ADDORREPLACEREADGROUPS as PICARD_ADDORREPLACEREADGROUPS_MT } from '../../../modules/nf-core/picard/addorreplacereadgroups/main'
Expand Down Expand Up @@ -32,10 +32,10 @@ workflow ALIGN_AND_CALL_MT {

BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, true)

SENTIEON_BWAMEM_MT ( ch_fastq, ch_fasta, ch_fai, ch_bwaindex )
SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta.map{ meta, fasta -> fasta }, ch_fai.map{ meta, fai -> fai } )

Channel.empty()
.mix(BWAMEM2_MEM_MT.out.bam, SENTIEON_BWAMEM_MT.out.bam)
.mix(BWAMEM2_MEM_MT.out.bam, SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, bai -> [meta, bam] })
.join(ch_ubam, failOnMismatch:true, failOnDuplicate:true)
.set {ch_bam_ubam}

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