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Merge pull request #257 from MaxUlysse/dsl2_updates
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updates on DSL2
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@FriederikeHanssen
FriederikeHanssen authored Jul 29, 2020
2 parents 538a296 + 6f3c37f commit f04833a
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Showing 25 changed files with 395 additions and 216 deletions.
54 changes: 54 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
/*
* -------------------------------------------------
* Nextflow config file for module specific-options
* -------------------------------------------------
*/

params {
modules {
'fastqc' {
args = "--quiet"
suffix = ""
publish_dir = "fastqc"
publish_results = "all"
}
'trimgalore' {
args = "--fastqc"
suffix = ""
publish_dir = "trimgalore"
publish_results = "all"
}
'bwamem2_index' {
args = ""
suffix = ""
publish_dir = "genome/bwa_index"
publish_results = "all"
}
'bwamem2_mem' {
args = "-K 100000000 -M"
args2 = ""
extra = ""
suffix = ""
publish_dir = ""
publish_results = "all"
}
'gatk_markduplicates' {
args = "ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
suffix = ".mLb.mkD"
publish_dir = "bwa/mergedLibrary"
publish_results = "all"
}
'get_software_versions' {
args = ""
suffix = ""
publish_dir = "pipeline_info"
publish_results = "all"
}
'output_documentation' {
args = ""
suffix = ""
publish_dir = "pipeline_info"
publish_results = "all"
}
}
}
26 changes: 13 additions & 13 deletions lib/Schema.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -78,22 +78,22 @@ class JSON {
return output
}

private static LinkedHashMap params_summary(workflow, params, run_name) {
private static LinkedHashMap params_summary(workflow, params, run_name, step, tools, skip_qc, annotate_tools) {
def Map summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = run_name ?: workflow.runName
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"

summary['Input'] = params.input
// summary['Step'] = step
summary['Step'] = step
summary['Genome'] = params.genome
// if (params.no_intervals && step != 'annotate') summary['Intervals'] = 'Do not use'
if (params.no_intervals && step != 'annotate') summary['Intervals'] = 'Do not use'
summary['Nucleotides/s'] = params.nucleotides_per_second
if (params.sentieon) summary['Sention'] = "Using Sentieon for Preprocessing and/or Variant Calling"
// if (params.skip_qc) summary['QC tools skipped'] = skip_qc.join(', ')
if (params.skip_qc) summary['QC tools skipped'] = skip_qc.join(', ')
if (params.target_bed) summary['Target BED'] = params.target_bed
// if (params.tools) summary['Tools'] = tools.join(', ')
if (params.tools) summary['Tools'] = tools.join(', ')
if (params.trim_fastq || params.split_fastq) summary['Modify fastqs'] = "trim and/or split"

if (params.trim_fastq) {
Expand All @@ -114,24 +114,24 @@ class JSON {
summary['Save BAMs mapped'] = params.save_bam_mapped ? 'Yes' : 'No'
summary['Skip MarkDuplicates'] = params.skip_markduplicates ? 'Yes' : 'No'

// if ('ascat' in tools) {
if ('ascat' in tools) {
summary['ASCAT'] = "Options"
if (params.ascat_purity) summary['purity'] = params.ascat_purity
if (params.ascat_ploidy) summary['ploidy'] = params.ascat_ploidy
// }
}

// if ('controlfreec' in tools) {
if ('controlfreec' in tools) {
summary['Control-FREEC'] = "Options"
if (params.cf_window) summary['window'] = params.cf_window
if (params.cf_coeff) summary['coeff of variation'] = params.cf_coeff
if (params.cf_ploidy) summary['ploidy'] = params.cf_ploidy
// }
}

// if ('haplotypecaller' in tools) summary['GVCF'] = params.no_gvcf ? 'No' : 'Yes'
// if ('strelka' in tools && 'manta' in tools) summary['Strelka BP'] = params.no_strelka_bp ? 'No' : 'Yes'
// if (params.pon && ('mutect2' in tools || (params.sentieon && 'tnscope' in tools))) summary['Panel of normals'] = params.pon
if ('haplotypecaller' in tools) summary['GVCF'] = params.no_gvcf ? 'No' : 'Yes'
if ('strelka' in tools && 'manta' in tools) summary['Strelka BP'] = params.no_strelka_bp ? 'No' : 'Yes'
if (params.pon && ('mutect2' in tools || (params.sentieon && 'tnscope' in tools))) summary['Panel of normals'] = params.pon

// if (params.annotate_tools) summary['Tools to annotate'] = annotate_tools.join(', ')
if (params.annotate_tools) summary['Tools to annotate'] = annotate_tools.join(', ')

if (params.annotation_cache) {
summary['Annotation cache'] = "Enabled"
Expand Down
165 changes: 95 additions & 70 deletions main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ if (params.help) {
include {
check_parameter_existence;
check_parameter_list;
define_anno_list;
define_skip_qc_list;
define_step_list;
define_tool_list;
Expand Down Expand Up @@ -90,20 +91,21 @@ skip_qc_list = define_skip_qc_list()
skip_qc = params.skip_qc ? params.skip_qc == 'all' ? skip_qc_list : params.skip_qc.split(',').collect{it.trim().toLowerCase().replaceAll('-', '').replaceAll('_', '')} : []
if (!check_parameter_list(skip_qc, skip_qc_list)) exit 1, 'Unknown QC tool(s), see --help for more information'

// anno_list = define_anno_list()
// annotate_tools = params.annotate_tools ? params.annotate_tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '')} : []
// if (!check_parameter_list(annotate_tools,anno_list)) exit 1, 'Unknown tool(s) to annotate, see --help for more information'
anno_list = define_anno_list()
annotate_tools = params.annotate_tools ? params.annotate_tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '')} : []
if (!check_parameter_list(annotate_tools,anno_list)) exit 1, 'Unknown tool(s) to annotate, see --help for more information'

// // Check parameters
// if ((params.ascat_ploidy && !params.ascat_purity) || (!params.ascat_ploidy && params.ascat_purity)) exit 1, 'Please specify both --ascat_purity and --ascat_ploidy, or none of them'
// if (params.cf_window && params.cf_coeff) exit 1, 'Please specify either --cf_window OR --cf_coeff, but not both of them'
if ((params.ascat_ploidy && !params.ascat_purity) || (!params.ascat_ploidy && params.ascat_purity)) exit 1, 'Please specify both --ascat_purity and --ascat_ploidy, or none of them'
if (params.cf_window && params.cf_coeff) exit 1, 'Please specify either --cf_window OR --cf_coeff, but not both of them'
if (params.umi && !(params.read_structure1 && params.read_structure2)) exit 1, 'Please specify both --read_structure1 and --read_structure2, when using --umi'

// Handle input
tsv_path = null
if (params.input && (has_extension(params.input, "tsv") || has_extension(params.input, "vcf") || has_extension(params.input, "vcf.gz"))) tsv_path = params.input
if (params.input && (has_extension(params.input, "vcf") || has_extension(params.input, "vcf.gz"))) step = "annotate"

// save_bam_mapped = params.skip_markduplicates ? true : params.save_bam_mapped ? true : false
save_bam_mapped = params.skip_markduplicates ? true : params.save_bam_mapped ? true : false

// If no input file specified, trying to get TSV files corresponding to step in the TSV directory
// only for steps preparerecalibration, recalibrate, variantcalling and controlfreec
Expand Down Expand Up @@ -175,7 +177,6 @@ if (tsv_path) {
*/

// Initialize each params in params.genomes, catch the command line first if it was defined

params.ac_loci = params.genome ? params.genomes[params.genome].ac_loci ?: false : false
params.ac_loci_gc = params.genome ? params.genomes[params.genome].ac_loci_gc ?: false : false
params.bwa = params.genome ? params.genomes[params.genome].bwa ?: false : false
Expand All @@ -196,7 +197,7 @@ params.snpeff_db = params.genome ? params.genomes[params.genome].s
params.species = params.genome ? params.genomes[params.genome].species ?: false : false
params.vep_cache_version = params.genome ? params.genomes[params.genome].vep_cache_version ?: false : false

// Initialize file channels based on params
// Initialize file channels based on params, defined in the params.genomes[params.genome] scope
chr_dir = params.chr_dir ?: Channel.empty()
chr_length = params.chr_length ?: Channel.empty()
dbsnp = params.dbsnp ?: Channel.empty()
Expand All @@ -206,21 +207,25 @@ known_indels = params.known_indels ?: Channel.empty()
loci = params.ac_loci ?: Channel.empty()
loci_gc = params.ac_loci_gc ?: Channel.empty()
mappability = params.mappability ?: Channel.empty()
pon = params.pon ?: Channel.empty()

// Initialize value channels based on params
snpeff_cache = params.snpeff_cache ?: Channel.empty()
// Initialize value channels based on params, defined in the params.genomes[params.genome] scope
snpeff_db = params.snpeff_db ?: Channel.empty()
snpeff_species = params.species ?: Channel.empty()
vep_cache = params.vep_cache ?: Channel.empty()
vep_cache_version = params.vep_cache_version ?: Channel.empty()

// Optional files, not defined within the params.genomes[params.genome] scope
cadd_indels = params.cadd_indels ?: Channel.empty()
cadd_indels_tbi = params.cadd_indels_tbi ?: Channel.empty()
cadd_wg_snvs = params.cadd_wg_snvs ?: Channel.empty()
cadd_wg_snvs_tbi = params.cadd_wg_snvs_tbi ?: Channel.empty()
target_bed = params.target_bed ?: Channel.empty()
// Initialize files channels based on params, not defined within the params.genomes[params.genome] scope
cadd_indels = params.cadd_indels ?: Channel.empty()
cadd_indels_tbi = params.cadd_indels_tbi ?: Channel.empty()
cadd_wg_snvs = params.cadd_wg_snvs ?: Channel.empty()
cadd_wg_snvs_tbi = params.cadd_wg_snvs_tbi ?: Channel.empty()
pon = params.pon ?: Channel.empty()
snpeff_cache = params.snpeff_cache ?: Channel.empty()
target_bed = params.target_bed ?: Channel.empty()
vep_cache = params.vep_cache ?: Channel.empty()

// Initialize value channels based on params, not defined within the params.genomes[params.genome] scope
read_structure1 = params.read_structure1 ?: Channel.empty()
read_structure2 = params.read_structure2 ?: Channel.empty()

/*
================================================================================
Expand All @@ -234,7 +239,7 @@ run_name = params.name
if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
run_name = workflow.runName
}
summary = Schema.params_summary(workflow, params, run_name)
summary = Schema.params_summary(workflow, params, run_name, step, tools, skip_qc, annotate_tools)
log.info Headers.nf_core(workflow, params.monochrome_logs)
log.info summary.collect { k,v -> "${k.padRight(20)}: $v" }.join("\n")
log.info "-\033[2m----------------------------------------------------\033[0m-"
Expand All @@ -252,30 +257,38 @@ if (params.sentieon) log.warn "[nf-core/sarek] Sentieon will be used, only works
================================================================================
*/

include { BWAMEM2_MEM } from './modules/local/bwamem2_mem.nf'
include { GET_SOFTWARE_VERSIONS } from './modules/local/get_software_versions'
include { OUTPUT_DOCUMENTATION } from './modules/local/output_documentation'
include { TRIM_GALORE } from './modules/local/trim_galore.nf'
include { MERGE_BAM_MAPPED } from './modules/local/merge_mapped_bam'
include { MARK_DUPLICATES } from './modules/local/mark_duplicates' addParams(skip_qc: skip_qc)
//include { BASE_RECALIBRATION } from './modules/local/base_recalibration' params(params)
include { BWAMEM2_MEM } from './modules/local/process/bwamem2_mem'
include { GET_SOFTWARE_VERSIONS } from './modules/local/process/get_software_versions'
include { OUTPUT_DOCUMENTATION } from './modules/local/process/output_documentation'
include { MERGE_BAM as MERGE_BAM_MAPPED;
MERGE_BAM as MERGE_BAM_RECAL;} from './modules/local/process/merge_bam'

/*
================================================================================
INCLUDE LOCAL PIPELINE SUBWORKFLOWS
================================================================================
*/

include { BUILD_INDICES } from './modules/subworkflows/build_indices'
include { BUILD_INDICES } from './modules/local/subworkflow/build_indices'

/*
================================================================================
INCLUDE nf-core PIPELINE MODULES
================================================================================
*/

include { FASTQC } from './modules/nf-core/fastqc'
include { MULTIQC } from './modules/nf-core/multiqc'
include { GATK_BASERECALIBRATOR as BASERECALIBRATOR } from './modules/nf-core/software/gatk_baserecalibrator'
include { GATK_GATHERBQSRREPORTS as GATHERBQSRREPORTS } from './modules/nf-core/software/gatk_gatherbqsrreports'
include { GATK_MARKDUPLICATES as MARKDUPLICATES } from './modules/nf-core/software/gatk_markduplicates'
include { MULTIQC } from './modules/nf-core/software/multiqc'

/*
================================================================================
INCLUDE nf-core PIPELINE SUBWORKFLOWS
================================================================================
*/

include { QC_TRIM } from './modules/nf-core/subworkflow/qc_trim'

// PREPARING CHANNELS FOR PREPROCESSING AND QC

Expand Down Expand Up @@ -338,38 +351,25 @@ workflow {
bwa = params.bwa ?: BUILD_INDICES.out.bwa
dbsnp_tbi = params.dbsnp ? params.dbsnp_index ?: BUILD_INDICES.out.dbsnp_tbi : Channel.empty()
dict = params.dict ?: BUILD_INDICES.out.dict
fai = params.fasta_fai ? params.fasta_fai : BUILD_INDICES.out.fai
fai = params.fasta_fai ?: BUILD_INDICES.out.fai
germline_resource_tbi = params.germline_resource ? params.germline_resource_index ?: BUILD_INDICES.out.germline_resource_tbi : Channel.empty()
intervals_bed = BUILD_INDICES.out.intervals_bed
intervals = BUILD_INDICES.out.intervals
known_indels_tbi = params.known_indels ? params.known_indels_index ?: BUILD_INDICES.out.known_indels_tbi.collect() : Channel.empty()
pon_tbi = params.pon ? params.pon_index ?: BUILD_INDICES.out.pon_tbi : Channel.empty()

// PREPROCESSING

fastqc_html = Channel.empty()
fastqc_version = Channel.empty()
fastqc_zip = Channel.empty()

if (!('fastqc' in skip_qc)) {
FASTQC(input_sample)
fastqc_html = FASTQC.out.html
fastqc_version = FASTQC.out.version
fastqc_zip = FASTQC.out.zip
}

def bwamem2_mem_options = [:]
QC_TRIM(
input_sample,
('fastqc' in skip_qc),
!(params.trim_fastq),
params.modules['fastqc'],
params.modules['trimgalore']
)

bwamem2_mem_options.args_bwamem2 = "-K 100000000 -M"
trim_galore_report = Channel.empty()

if (params.trim_fastq) {
TRIM_GALORE(input_sample)
BWAMEM2_MEM(TRIM_GALORE.out.trimmed_reads, bwa, fasta, fai, bwamem2_mem_options)
trim_galore_report = TRIM_GALORE.out.report
}
else BWAMEM2_MEM(input_sample, bwa, fasta, fai, bwamem2_mem_options)
BWAMEM2_MEM(QC_TRIM.out.reads, bwa, fasta, fai, params.modules['bwamem2_mem'])

results = BWAMEM2_MEM.out.map{ meta, bam, bai ->
BWAMEM2_MEM.out.map{ meta, bam, bai ->
patient = meta.patient
sample = meta.sample
gender = meta.gender
Expand All @@ -379,7 +379,7 @@ workflow {
.branch{
single: it[4].size() == 1
multiple: it[4].size() > 1
}.set { bam }
}.set{ bam }

bam_single = bam.single.map {
patient, sample, gender, status, bam, bai ->
Expand Down Expand Up @@ -411,35 +411,60 @@ workflow {

bam_mapped = bam_single.mix(MERGE_BAM_MAPPED(bam_multiple))

bam_mapped.view()

mark_duplicates_report = Channel.empty()
bam_duplicates_marked = Channel.empty()
report_markduplicates = Channel.empty()
bam_markduplicates = bam_mapped

if (!(params.skip_markduplicates)) {
// MARK_DUPLICATES(bam_mapped)
// mark_duplicates_report = MARK_DUPLICATES.out.report
// bam_duplicates_marked = MARK_DUPLICATES.out.bam
MARKDUPLICATES(bam_mapped)
report_markduplicates = MARKDUPLICATES.out.report
bam_markduplicates = MARKDUPLICATES.out.bam
}

bam_baserecalibrator = bam_markduplicates.combine(BUILD_INDICES.out.intervals)

BASERECALIBRATOR(bam_baserecalibrator, dbsnp, dbsnp_tbi, dict, fai, fasta, known_indels, known_indels_tbi)

if (!params.no_intervals) {
BASERECALIBRATOR.out.report.map{ meta, table ->
patient = meta.patient
sample = meta.sample
gender = meta.gender
status = meta.status
[patient, sample, gender, status, table]
}.groupTuple(by: [0,1]).set{ recaltable }

recaltable = recaltable.map {
patient, sample, gender, status, recal ->

def meta = [:]
meta.patient = patient
meta.sample = sample
meta.gender = gender[0]
meta.status = status[0]
meta.id = sample

[meta, recal]
}

GATHERBQSRREPORTS(recaltable)
}

// bamBaseRecalibrator = bam_duplicates_marked.combine(BUILD_INDICES.out.intervals_bed)

// //BASE_RECALIBRATION(bamBaseRecalibrator,dbsnp, dbsnp_index,fasta,)

OUTPUT_DOCUMENTATION(
output_docs,
output_docs_images)

GET_SOFTWARE_VERSIONS()

MULTIQC(
fastqc_html.collect().ifEmpty([]),
fastqc_zip.collect().ifEmpty([]),
GET_SOFTWARE_VERSIONS.out.yml,
QC_TRIM.out.fastqc_html.collect().ifEmpty([]),
QC_TRIM.out.fastqc_zip.collect().ifEmpty([]),
QC_TRIM.out.trimgalore_html.collect().ifEmpty([]),
QC_TRIM.out.trimgalore_log.collect().ifEmpty([]),
QC_TRIM.out.trimgalore_zip.collect().ifEmpty([]),
multiqc_config,
multiqc_custom_config.ifEmpty([]),
GET_SOFTWARE_VERSIONS.out.yml,
trim_galore_report.collect().ifEmpty([]),
mark_duplicates_report.collect().ifEmpty([]),
report_markduplicates.collect().ifEmpty([]),
workflow_summary)
}

Expand Down
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