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Implemented MSISENSORPRO tumor-only analysis #1737

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Implemented MSISENSORPRO tumor-only analysis #1737

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10 changes: 10 additions & 0 deletions conf/modules/msisensorpro.config
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Expand Up @@ -22,4 +22,14 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'MSISENSORPRO_MSITUMORONLY' {
ext.args = { params.wes ? '-c 20' : '-c 15' } // default values by MSIsensorpro
ext.prefix = { "${meta.id}.tumor_only" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/msisensorpro/${meta.id}/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
19 changes: 16 additions & 3 deletions main.nf
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Expand Up @@ -77,6 +77,7 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nf
include { PREPARE_GENOME } from './subworkflows/local/prepare_genome'
include { PREPARE_INTERVALS } from './subworkflows/local/prepare_intervals'
include { PREPARE_REFERENCE_CNVKIT } from './subworkflows/local/prepare_reference_cnvkit'
include { MSISENSORPRO_SCAN } from './modules/nf-core/msisensorpro/scan/main'

// Initialize fasta file with meta map:
fasta = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty()
Expand All @@ -91,6 +92,7 @@ germline_resource = params.germline_resource ? Channel.fromPath(para
known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.value([])
known_snps = params.known_snps ? Channel.fromPath(params.known_snps).collect() : Channel.value([])
mappability = params.mappability ? Channel.fromPath(params.mappability).collect() : Channel.value([])
msisensorpro_baseline = params.msisensorpro_baseline ? Channel.fromPath(params.msisensorpro_baseline).collect() : Channel.empty()
pon = params.pon ? Channel.fromPath(params.pon).collect() : Channel.value([]) // PON is optional for Mutect2 (but highly recommended)
sentieon_dnascope_model = params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect() : Channel.value([])

Expand Down Expand Up @@ -166,8 +168,18 @@ workflow NFCORE_SAREK {
aligner == "bwa-mem2" ? bwamem2 :
dragmap

// TODO: add a params for msisensorpro_scan
msisensorpro_scan = PREPARE_GENOME.out.msisensorpro_scan
// Reference msi list for MSIsensorpro
if (params.tools && params.tools.split(',').contains('msisensorpro')) {
if (params.msisensorpro_scan) {
msisensorpro_scan = Channel.fromPath(params.msisensorpro_scan).collect()
} else {
MSISENSORPRO_SCAN(fasta)
msisensorpro_scan = MSISENSORPRO_SCAN.out.list.map{ meta, list -> [list] }
versions = versions.mix(MSISENSORPRO_SCAN.out.versions)
Comment on lines +176 to +178
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Is this something we can put in the PREPARE* subworkflows together with other reference computations for tools?

}
} else {
msisensorpro_scan = Channel.empty()
}

// For ASCAT, extracted from zip or tar.gz files
allele_files = PREPARE_GENOME.out.allele_files
Expand All @@ -177,7 +189,7 @@ workflow NFCORE_SAREK {
rt_file = PREPARE_GENOME.out.rt_file

// Tabix indexed vcf files
bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.value([])
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merged your PR, so If you merge in dev this should hopefully be fixed already

dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi).collect() : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([])
Expand Down Expand Up @@ -296,6 +308,7 @@ workflow NFCORE_SAREK {
loci_files,
mappability,
msisensorpro_scan,
msisensorpro_baseline,
ngscheckmate_bed,
pon,
pon_tbi,
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/msisensorpro/msisomatic/main.nf
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6 changes: 1 addition & 5 deletions modules/nf-core/msisensorpro/msisomatic/meta.yml
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7 changes: 7 additions & 0 deletions modules/nf-core/msisensorpro/msitumoronly/environment.yml
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46 changes: 46 additions & 0 deletions modules/nf-core/msisensorpro/msitumoronly/main.nf
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68 changes: 68 additions & 0 deletions modules/nf-core/msisensorpro/msitumoronly/meta.yml
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2 changes: 2 additions & 0 deletions nextflow.config
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Expand Up @@ -71,6 +71,8 @@ params {
ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2
joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected
joint_mutect2 = false // if true, enables patient-wise multi-sample somatic variant calling
msisensorpro_scan = null // by default the reference is build from the fasta file
msisensorpro_baseline = null // by default tumor-only mode is not used in MSIsensorpro
only_paired_variant_calling = false // if true, skips germline variant calling for normal-paired sample
sentieon_dnascope_emit_mode = 'variant' // default value for Sentieon dnascope
sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE'
Expand Down
10 changes: 10 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -733,6 +733,16 @@
"hidden": true,
"help_text": "If you use AWS iGenomes, this has already been set for you appropriately."
},
"msisensorpro_scan": {
"type": "string",
"fa_icon": "fas fa-file-alt",
"description": "Path to MSIsensorpro reference genome microsatellites information file."
},
"msisensorpro_baseline": {
"type": "string",
"fa_icon": "fas fa-file-alt",
"description": "Path to MSIsensorpro custom baseline file for tumor-only analysis."
},
"ngscheckmate_bed": {
"type": "string",
"fa_icon": "fas fa-file",
Expand Down
9 changes: 3 additions & 6 deletions subworkflows/local/bam_variant_calling_somatic_all/main.nf
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Expand Up @@ -44,13 +44,12 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
wes // boolean: [mandatory] [default: false] whether targeted data is processed

main:
versions = Channel.empty()
versions = Channel.empty()

//TODO: Temporary until the if's can be removed and printing to terminal is prevented with "when" in the modules.config
vcf_freebayes = Channel.empty()
vcf_manta = Channel.empty()
vcf_strelka = Channel.empty()
out_msisensorpro = Channel.empty()
vcf_mutect2 = Channel.empty()
vcf_tiddit = Channel.empty()

Expand Down Expand Up @@ -175,11 +174,10 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
}

// MSISENSOR
if (tools.split(',').contains('msisensorpro')) {
if (tools.split(',').contains('msisensorpro') && msisensorpro_scan) {
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This should not be strictly necessary since the empty channel should skip the tool

MSISENSORPRO_MSISOMATIC(cram.combine(intervals_bed_combined), fasta.map{ meta, fasta -> [ fasta ] }, msisensorpro_scan)

versions = versions.mix(MSISENSORPRO_MSISOMATIC.out.versions)
out_msisensorpro = out_msisensorpro.mix(MSISENSORPRO_MSISOMATIC.out.output_report)
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any reason you are not emitting the output of the workflow anymore?

}

// MUTECT2
Expand All @@ -190,7 +188,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
// joint_mutect2 mode needs different meta.map than regular mode
cram.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai ->
joint_mutect2 ?
//we need to keep all fields and then remove on a per-tool-basis to ensure proper joining at the filtering step
// we need to keep all fields and then remove on a per-tool-basis to ensure proper joining at the filtering step
[ meta + [ id:meta.patient ], [ normal_cram, tumor_cram ], [ normal_crai, tumor_crai ] ] :
[ meta, [ normal_cram, tumor_cram ], [ normal_crai, tumor_crai ] ]
},
Expand Down Expand Up @@ -232,7 +230,6 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
)

emit:
out_msisensorpro
vcf_all
vcf_freebayes
vcf_manta
Expand Down
23 changes: 16 additions & 7 deletions subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
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Expand Up @@ -11,6 +11,7 @@ include { BAM_VARIANT_CALLING_SINGLE_TIDDIT } from '../bam_variant_cal
include { BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC } from '../bam_variant_calling_tumor_only_controlfreec/main'
include { BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA } from '../bam_variant_calling_tumor_only_manta/main'
include { BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2 } from '../bam_variant_calling_tumor_only_mutect2/main'
include { MSISENSORPRO_MSITUMORONLY } from '../../../modules/nf-core/msisensorpro/msitumoronly/main'

workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
take:
Expand All @@ -32,21 +33,22 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped
intervals_bed_gz_tbi_combined // channel: [mandatory] intervals/target regions in one file zipped
mappability
msisensorpro_baseline // channel: [optional] msisensorpro_baseline
panel_of_normals // channel: [optional] panel_of_normals
panel_of_normals_tbi // channel: [optional] panel_of_normals_tbi
joint_mutect2 // boolean: [mandatory] [default: false] run mutect2 in joint mode
wes // boolean: [mandatory] [default: false] whether targeted data is processed

main:
versions = Channel.empty()
versions = Channel.empty()

//TODO: Temporary until the if's can be removed and printing to terminal is prevented with "when" in the modules.config
vcf_freebayes = Channel.empty()
vcf_manta = Channel.empty()
vcf_mpileup = Channel.empty()
vcf_mutect2 = Channel.empty()
vcf_strelka = Channel.empty()
vcf_tiddit = Channel.empty()
vcf_freebayes = Channel.empty()
vcf_manta = Channel.empty()
vcf_mpileup = Channel.empty()
vcf_mutect2 = Channel.empty()
vcf_strelka = Channel.empty()
vcf_tiddit = Channel.empty()

// MPILEUP
if (tools.split(',').contains('mpileup') || tools.split(',').contains('controlfreec')) {
Expand Down Expand Up @@ -109,6 +111,13 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
versions = versions.mix(BAM_VARIANT_CALLING_FREEBAYES.out.versions)
}

// MSISENSOR
if (tools.split(',').contains('msisensorpro') && msisensorpro_baseline) {
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similar here, if the baseline is require than the tool shouldn't run on an empty channel

MSISENSORPRO_MSITUMORONLY(cram.combine(intervals_bed_combined), fasta.map{ meta, fasta -> [ fasta ] }, msisensorpro_baseline)

versions = versions.mix(MSISENSORPRO_MSITUMORONLY.out.versions)
}

// MUTECT2
if (tools.split(',').contains('mutect2')) {
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2(
Expand Down
4 changes: 0 additions & 4 deletions subworkflows/local/prepare_genome/main.nf
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Expand Up @@ -12,7 +12,6 @@ include { BWA_INDEX as BWAMEM1_INDEX } from '../../../modules/nf-
include { BWAMEM2_INDEX } from '../../../modules/nf-core/bwamem2/index/main'
include { DRAGMAP_HASHTABLE } from '../../../modules/nf-core/dragmap/hashtable/main'
include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main'
include { MSISENSORPRO_SCAN } from '../../../modules/nf-core/msisensorpro/scan/main'
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what is the reason to move this out?

include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main'
include { TABIX_TABIX as TABIX_BCFTOOLS_ANNOTATIONS } from '../../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main'
Expand Down Expand Up @@ -50,7 +49,6 @@ workflow PREPARE_GENOME {
DRAGMAP_HASHTABLE(fasta) // If aligner is dragmap

GATK4_CREATESEQUENCEDICTIONARY(fasta)
MSISENSORPRO_SCAN(fasta)
SAMTOOLS_FAIDX(fasta, [ [ id:'no_fai' ], [] ] )

// the following are flattened and mapped in case the user supplies more than one value for the param
Expand Down Expand Up @@ -105,7 +103,6 @@ workflow PREPARE_GENOME {
versions = versions.mix(BWAMEM2_INDEX.out.versions)
versions = versions.mix(DRAGMAP_HASHTABLE.out.versions)
versions = versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions)
versions = versions.mix(MSISENSORPRO_SCAN.out.versions)
versions = versions.mix(SAMTOOLS_FAIDX.out.versions)
versions = versions.mix(TABIX_BCFTOOLS_ANNOTATIONS.out.versions)
versions = versions.mix(TABIX_DBSNP.out.versions)
Expand All @@ -125,7 +122,6 @@ workflow PREPARE_GENOME {
germline_resource_tbi = TABIX_GERMLINE_RESOURCE.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: germline_resource.vcf.gz.tbi
known_snps_tbi = TABIX_KNOWN_SNPS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi
known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi
msisensorpro_scan = MSISENSORPRO_SCAN.out.list.map{ meta, list -> [list] } // path: genome_msi.list
pon_tbi = TABIX_PON.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: pon.vcf.gz.tbi

allele_files // path: allele_files
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/samplesheet_to_channel/main.nf
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Expand Up @@ -153,7 +153,7 @@ workflow SAMPLESHEET_TO_CHANNEL{
}

input_sample.filter{ it[0].status == 0 }.ifEmpty{ // In this case, the sample-sheet contains no normal/germline-samples
def tools_requiring_normal_samples = ['ascat', 'deepvariant', 'haplotypecaller', 'msisensorpro']
def tools_requiring_normal_samples = ['ascat', 'deepvariant', 'haplotypecaller']
def requested_tools_requiring_normal_samples = []
tools_requiring_normal_samples.each{ tool_requiring_normal_samples ->
if (tools.split(',').contains(tool_requiring_normal_samples)) requested_tools_requiring_normal_samples.add(tool_requiring_normal_samples)
Expand All @@ -164,7 +164,7 @@ workflow SAMPLESHEET_TO_CHANNEL{
}
}

// Fails when wrongfull extension for intervals file
// Fails when wrongful extension for intervals file
if (wes && !step == 'annotate') {
if (intervals && !intervals.endsWith("bed")) error("Target file specified with `--intervals` must be in BED format for targeted data")
else log.warn("Intervals file was provided without parameter `--wes`: Pipeline will assume this is Whole-Genome-Sequencing data.")
Expand Down
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