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Add gatk somatic tumour calling subworkflow (#1064)
* initial commit to set up new branch * save changes to checkout * workflow working, still needs test.yml and meta.yml, also fix versions file * subworkflow finished * Update pytest_subworkflows.yml * Update pytest_subworkflows.yml * Update pytest_subworkflows.yml * fix config subworkflow name * Update main.nf * Update pytest_subworkflows.yml * fixed md5sum issue likely caused by gatk version update * tumour changed to tumor * old dir deleted * Comments added to explain use of placeholders '[]' * updated index names, input channel renamed to input * Apply suggestions from code review * updated to perform new subworkflow testing Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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GCJMackenzie
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6 changed files with 264 additions and 4 deletions
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//
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// Run GATK mutect2 in tumor only mode, getepileupsummaries, calculatecontamination and filtermutectcalls
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//
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params.mutect2_options = [:]
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params.getpileup_options = [:]
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params.calccontam_options = [:]
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params.filtercalls_options = [suffix: '_filtered']
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include { GATK4_MUTECT2 as MUTECT2 } from '../../../modules/gatk4/mutect2/main' addParams( options: params.mutect2_options )
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include { GATK4_GETPILEUPSUMMARIES as GETPILEUPSUMMARIES } from '../../../modules/gatk4/getpileupsummaries/main' addParams( options: params.getpileup_options )
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include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION } from '../../../modules/gatk4/calculatecontamination/main' addParams( options: params.calccontam_options )
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include { GATK4_FILTERMUTECTCALLS as FILTERMUTECTCALLS } from '../../../modules/gatk4/filtermutectcalls/main' addParams( options: params.filtercalls_options )
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workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
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take:
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input // channel: [ val(meta), [ input ], [ input_index ], [] ]
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fasta // channel: /path/to/reference/fasta
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fai // channel: /path/to/reference/fasta/index
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dict // channel: /path/to/reference/fasta/dictionary
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germline_resource // channel: /path/to/germline/resource
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germline_resource_tbi // channel: /path/to/germline/index
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panel_of_normals // channel: /path/to/panel/of/normals
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panel_of_normals_tbi // channel: /path/to/panel/of/normals/index
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interval_file // channel: /path/to/interval/file
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main:
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ch_versions = Channel.empty()
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mutect2_input = channel.from(input)
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//
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//Perform variant calling using mutect2 module in tumor single mode.
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//
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MUTECT2 ( mutect2_input , true , false , false , [] , fasta , fai , dict , germline_resource , germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
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ch_versions = ch_versions.mix(MUTECT2.out.versions)
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//
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//Generate pileup summary table using getepileupsummaries.
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//
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pileup_input = channel.from(input).map {
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meta, input_file, input_index, which_norm ->
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[meta, input_file[0], input_index[0]]
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}
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GETPILEUPSUMMARIES ( pileup_input , germline_resource , germline_resource_tbi , interval_file )
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ch_versions = ch_versions.mix(GETPILEUPSUMMARIES.out.versions)
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//
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//Contamination and segmentation tables created using calculatecontamination on the pileup summary table.
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//
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ch_pileup = GETPILEUPSUMMARIES.out.table.collect()
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//[] is a placeholder for the optional input where the matched normal sample would be passed in for tumor-normal samples, which is not necessary for this workflow.
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ch_pileup.add([])
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CALCULATECONTAMINATION ( ch_pileup, true )
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ch_versions = ch_versions.mix(CALCULATECONTAMINATION.out.versions)
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//
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//Mutect2 calls filtered by filtermutectcalls using the contamination and segmentation tables.
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//
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ch_vcf = MUTECT2.out.vcf.collect()
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ch_tbi = MUTECT2.out.tbi.collect()
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ch_stats = MUTECT2.out.stats.collect()
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//[] is added as a placeholder for the optional input file artifact priors, which is only used for tumor-normal samples and therefor isn't needed in this workflow.
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ch_stats.add([])
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ch_segment = CALCULATECONTAMINATION.out.segmentation.collect()
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ch_contamination = CALCULATECONTAMINATION.out.contamination.collect()
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//[] is added as a placeholder for entering a contamination estimate value, which is not needed as this workflow uses the contamination table instead.
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ch_contamination.add([])
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ch_filtermutect_in = ch_vcf.combine(ch_tbi, by: 0).combine(ch_stats, by: 0).combine(ch_segment, by: 0).combine(ch_contamination, by: 0)
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FILTERMUTECTCALLS ( ch_filtermutect_in, fasta, fai, dict )
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ch_versions = ch_versions.mix(FILTERMUTECTCALLS.out.versions)
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emit:
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mutect2_vcf = MUTECT2.out.vcf.collect() // channel: [ val(meta), [ vcf ] ]
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mutect2_index = MUTECT2.out.tbi.collect() // channel: [ val(meta), [ tbi ] ]
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mutect2_stats = MUTECT2.out.stats.collect() // channel: [ val(meta), [ stats ] ]
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pileup_table = GETPILEUPSUMMARIES.out.table.collect() // channel: [ val(meta), [ table ] ]
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contamination_table = CALCULATECONTAMINATION.out.contamination.collect() // channel: [ val(meta), [ contamination ] ]
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segmentation_table = CALCULATECONTAMINATION.out.segmentation.collect() // channel: [ val(meta), [ segmentation ] ]
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filtered_vcf = FILTERMUTECTCALLS.out.vcf.collect() // channel: [ val(meta), [ vcf ] ]
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filtered_index = FILTERMUTECTCALLS.out.tbi.collect() // channel: [ val(meta), [ tbi ] ]
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filtered_stats = FILTERMUTECTCALLS.out.stats.collect() // channel: [ val(meta), [ stats ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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name: gatk_tumor_only_somatic_variant_calling
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description: |
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Perform variant calling on a single tumor sample using mutect2 tumor only mode.
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Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables.
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Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.
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keywords:
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- gatk4
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- mutect2
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- getpileupsummaries
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- calculatecontamination
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- filtermutectcalls
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- variant_calling
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- tumor_only
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- filtered_vcf
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modules:
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- gatk4/mutect2
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- gatk4/getpileupsummaries
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- gatk4/calculatecontamination
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- gatk4/filtermutectcalls
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- input:
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type: list
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description: list containing one BAM file, also able to take CRAM as an input
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pattern: "[ *.{bam/cram} ]"
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- input_index:
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type: list
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description: list containing one BAM file indexe, also able to take CRAM index as an input
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pattern: "[ *.{bam.bai/cram.crai} ]"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- germline_resource:
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type: file
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description: Population vcf of germline sequencing, containing allele fractions.
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pattern: "*.vcf.gz"
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- germline_resource_tbi:
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type: file
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description: Index file for the germline resource.
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pattern: "*.vcf.gz.tbi"
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- panel_of_normals:
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type: file
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description: vcf file to be used as a panel of normals.
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pattern: "*.vcf.gz"
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- panel_of_normals_tbi:
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type: file
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description: Index for the panel of normals.
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pattern: "*.vcf.gz.tbi"
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- interval_file:
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type: file
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description: File containing intervals.
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pattern: "*.interval_list"
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output:
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- versions:
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type: file
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description: File containing software versions
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pattern: 'versions.yml'
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- mutect2_vcf:
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type: file
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description: Compressed vcf file to be used for variant_calling.
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pattern: "[ *.vcf.gz ]"
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- mutect2_tbi:
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type: file
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description: Indexes of the mutect2_vcf file
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pattern: "[ *vcf.gz.tbi ]"
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- mutect2_stats:
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type: file
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description: Stats files for the mutect2 vcf
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pattern: "[ *vcf.gz.stats ]"
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- pileup_table:
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type: file
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description: File containing the pileup summary table.
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pattern: "*.pileups.table"
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- contamination_table:
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type: file
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description: File containing the contamination table.
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pattern: "*.contamination.table"
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- segmentation_table:
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type: file
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description: Output table containing segmentation of tumor minor allele fractions.
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pattern: "*.segmentation.table"
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- filtered_vcf:
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type: file
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description: file containing filtered mutect2 calls.
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pattern: "*.vcf.gz"
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- filtered_tbi:
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type: file
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description: tbi file that pairs with filtered vcf.
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pattern: "*.vcf.gz.tbi"
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- filtered_stats:
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type: file
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description: file containing statistics of the filtermutectcalls run.
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pattern: "*.filteringStats.tsv"
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authors:
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- '@GCJMackenzie'
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params.mutect2_options = [:]
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params.getpileup_options = [:]
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params.calccontam_options = [:]
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params.filtercalls_options = [:]
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@ -474,7 +474,7 @@ gatk4/bedtointervallist:
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- modules/gatk4/bedtointervallist/**
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- tests/modules/gatk4/bedtointervallist/**
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gatk4/calculatecontamination:
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gatk4/calculatecontamination: &gatk4/calculatecontamination
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- modules/gatk4/calculatecontamination/**
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- tests/modules/gatk4/calculatecontamination/**
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- modules/gatk4/fastqtosam/**
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- tests/modules/gatk4/fastqtosam/**
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gatk4/filtermutectcalls:
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gatk4/filtermutectcalls: &gatk4/filtermutectcalls
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- modules/gatk4/filtermutectcalls/**
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- tests/modules/gatk4/filtermutectcalls/**
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@ -506,7 +506,7 @@ gatk4/genotypegvcfs:
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- modules/gatk4/genotypegvcfs/**
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- tests/modules/gatk4/genotypegvcfs/**
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gatk4/getpileupsummaries:
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gatk4/getpileupsummaries: &gatk4/getpileupsummaries
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- modules/gatk4/getpileupsummaries/**
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- tests/modules/gatk4/getpileupsummaries/**
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@ -538,7 +538,7 @@ gatk4/mergevcfs:
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- modules/gatk4/mergevcfs/**
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- tests/modules/gatk4/mergevcfs/**
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gatk4/mutect2:
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gatk4/mutect2: &gatk4/mutect2
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- modules/gatk4/mutect2/**
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- tests/modules/gatk4/mutect2/**
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@ -1426,3 +1426,11 @@ subworkflows/gatk_create_som_pon:
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- tests/subworkflows/nf-core/gatk_create_som_pon/**
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- *gatk4/genomicsdbimport
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- *gatk4/createsomaticpanelofnormals
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subworkflows/gatk_tumor_only_somatic_variant_calling:
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- subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
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- tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
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- *gatk4/mutect2
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- *gatk4/getpileupsummaries
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- *gatk4/calculatecontamination
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- *gatk4/filtermutectcalls
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING } from '../../../../subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/main' addParams( [:] )
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workflow test_gatk_tumor_only_somatic_variant_calling {
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input = [
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[[ id:'test' ], // meta map
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[file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
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[file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
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[] ]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
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germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
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panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
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panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
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interval_file = file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true)
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GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi, interval_file )
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}
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- name: gatk_tumor_only_somatic_variant_calling
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command: nextflow run ./tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling -entry test_gatk_tumor_only_somatic_variant_calling -c tests/config/nextflow.config
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tags:
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- subworkflows/gatk_tumor_only_somatic_variant_calling
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# Modules
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# - gatk4/mutect2
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# - gatk4/getpileupsummaries
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# - gatk4/calculatecontamination
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# - gatk4/filtermutectcalls
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files:
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# gatk4 mutect2
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- path: ./output/mutect2/test.vcf.gz
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- path: ./output/mutect2/test.vcf.gz.stats
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md5sum: 106c5828b02b906c97922618b6072169
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- path: ./output/mutect2/test.vcf.gz.tbi
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# gatk4 getpileupsummaries
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- path: ./output/getpileupsummaries/test.pileups.table
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md5sum: 8b1b4c8ab831eca50ee9e940463a741f
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# gatk4 calculatecontamination
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- path: ./output/calculatecontamination/test.contamination.table
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md5sum: 5fdcf1728cf98985ce31c038eb24e05c
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- path: ./output/calculatecontamination/test.segmentation.table
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md5sum: 91f28bfe4727a3256810927fc5eba92f
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# gatk4 filtermutectcalls
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- path: ./output/filtermutectcalls/test_filtered.vcf.gz
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- path: ./output/filtermutectcalls/test_filtered.vcf.gz.filteringStats.tsv
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md5sum: 8731945490960546719ce4a71a151e4f
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- path: ./output/filtermutectcalls/test_filtered.vcf.gz.tbi
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