Workflows

This page documents all workflows in the pipeline.

NFCORE_SAREK
(entry) (entry point)
SAREK
BAM_NGSCHECKMATE
UTILS_NFCORE_PIPELINE
UTILS_NEXTFLOW_PIPELINE
VCF_ANNOTATE_SNPEFF
UTILS_NFSCHEMA_PLUGIN
VCF_ANNOTATE_ENSEMBLVEP
BAM_VARIANT_CALLING_SOMATIC_MUTECT2
SAMPLESHEET_TO_CHANNEL
CHANNEL_VARIANT_CALLING_CREATE_CSV
BAM_VARIANT_CALLING_TUMOR_ONLY_LOFREQ
BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2
BAM_JOINT_CALLING_GERMLINE_SENTIEON
VCF_QC_BCFTOOLS_VCFTOOLS
BAM_VARIANT_CALLING_SENTIEON_DNASCOPE
BAM_VARIANT_CALLING_SOMATIC_MUSE
BAM_VARIANT_CALLING_FREEBAYES
CHANNEL_BASERECALIBRATOR_CREATE_CSV
BAM_VARIANT_CALLING_SOMATIC_MANTA
BAM_VARIANT_CALLING_TUMOR_ONLY_ALL
PREPARE_REFERENCE_CNVKIT
CONCATENATE_GERMLINE_VCFS
BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC
BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA
BAM_VARIANT_CALLING_SOMATIC_ALL
BAM_MARKDUPLICATES_SPARK
BAM_APPLYBQSR_SPARK
BAM_VARIANT_CALLING_SOMATIC_STRELKA
CHANNEL_MARKDUPLICATES_CREATE_CSV
BAM_VARIANT_CALLING_DEEPVARIANT
VCF_VARLOCIRAPTOR_SINGLE
CRAM_QC_MOSDEPTH_SAMTOOLS
DOWNLOAD_CACHE_SNPEFF_VEP
FASTQ_PREPROCESS_GATK
BAM_MERGE_INDEX_SAMTOOLS
FASTQ_PREPROCESS_PARABRICKS
VCF_VARIANT_FILTERING_GATK
BAM_CONVERT_SAMTOOLS
BAM_SENTIEON_DEDUP
BAM_VARIANT_CALLING_SOMATIC_TIDDIT
CHANNEL_ALIGN_CREATE_CSV
BAM_MARKDUPLICATES
CRAM_MERGE_INDEX_SAMTOOLS
ANNOTATION_CACHE_INITIALISATION
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER
BAM_VARIANT_CALLING_SINGLE_TIDDIT
BAM_VARIANT_CALLING_CNVKIT
CRAM_SAMPLEQC
CONSENSUS
BAM_VARIANT_CALLING_INDEXCOV
FASTQ_CREATE_UMI_CONSENSUS_FGBIO
BAM_VARIANT_CALLING_MPILEUP
BAM_VARIANT_CALLING_SINGLE_STRELKA
POST_VARIANTCALLING
VCF_VARLOCIRAPTOR_SOMATIC
BAM_VARIANT_CALLING_GERMLINE_MANTA
BAM_APPLYBQSR
BAM_VARIANT_CALLING_SOMATIC_TNSCOPE
NORMALIZE_VCFS
BAM_VARIANT_CALLING_TUMOR_ONLY_TNSCOPE
BAM_VARIANT_CALLING_HAPLOTYPECALLER
PIPELINE_INITIALISATION
PIPELINE_COMPLETION
PREPARE_GENOME
BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC
BAM_BASERECALIBRATOR_SPARK
BAM_BASERECALIBRATOR
BAM_JOINT_CALLING_GERMLINE_GATK
CHANNEL_APPLYBQSR_CREATE_CSV
FASTQ_ALIGN
BAM_VARIANT_CALLING_GERMLINE_ALL
VCF_ANNOTATE_ALL
BAM_VARIANT_CALLING_SOMATIC_ASCAT

NFCORE_SAREK

Defined in main.nf:86

Inputs

Name	Description
`samplesheet`	-

Outputs

Name	Description
`multiqc_report`	-

(entry)

Entry workflow

Defined in main.nf:298

SAREK

Defined in workflows/sarek/main.nf:63

Inputs

Name	Description
`input_sample`	-
`aligner`	-
`skip_tools`	-
`step`	-
`tools`	-
`ascat_alleles`	-
`ascat_loci`	-
`ascat_loci_gc`	-
`ascat_loci_rt`	-
`bbsplit_index`	-
`bcftools_annotations`	-
`bcftools_annotations_tbi`	-
`bcftools_columns`	-
`bcftools_header_lines`	-
`cf_chrom_len`	-
`chr_files`	-
`cnvkit_reference`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dbsnp_vqsr`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`germline_resource`	-
`germline_resource_tbi`	-
`index_alignment`	-
`intervals_and_num_intervals`	-
`intervals_bed_combined`	-
`intervals_bed_combined_for_variant_calling`	-
`intervals_bed_gz_tbi_and_num_intervals`	-
`intervals_bed_gz_tbi_combined`	-
`intervals_for_preprocessing`	-
`known_indels_vqsr`	-
`known_sites_indels`	-
`known_sites_indels_tbi`	-
`known_sites_snps`	-
`known_sites_snps_tbi`	-
`known_snps_vqsr`	-
`mappability`	-
`msisensor2_models`	-
`msisensorpro_scan`	-
`ngscheckmate_bed`	-
`pon`	-
`pon_tbi`	-
`sentieon_dnascope_model`	-
`varlociraptor_scenario_germline`	-
`varlociraptor_scenario_somatic`	-
`varlociraptor_scenario_tumor_only`	-
`snpeff_cache`	-
`snpeff_db`	-
`vep_cache`	-
`vep_cache_version`	-
`vep_extra_files`	-
`vep_fasta`	-
`vep_genome`	-
`vep_species`	-
`versions`	-

Outputs

Name	Description
`?`	-
`?`	-

BAM_NGSCHECKMATE

Defined in subworkflows/nf-core/bam_ngscheckmate/main.nf:4

Keywords: ngscheckmate, qc, bam, snp

Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.

Components

This workflow uses the following modules/subworkflows:

bcftools/mpileup
ngscheckmate/ncm

Inputs

Name	Description
`meta1`	Groovy Map containing sample information e.g. [ id:'test' ]
`bam`	BAM files for each sample
`meta2`	Groovy Map containing bed file information e.g. [ id:'sarscov2' ]
`snp_bed`	BED file containing the SNPs to analyse. NGSCheckMate provides some default ones for hg19/hg38.
`meta3`	Groovy Map containing reference genome meta information e.g. [ id:'sarscov2' ]
`fasta`	fasta file for the genome

Outputs

Name	Description
`pdf`	A pdf containing a dendrogram showing how the samples match up
`corr_matrix`	A text file containing the correlation matrix between each sample
`matched`	A txt file containing only the samples that match with each other
`all`	A txt file containing all the sample comparisons, whether they match or not
`vcf`	vcf files for each sample giving the SNP calls
`versions`	File containing software versions

Authors: @SPPearce Maintainers: @SPPearce

UTILS_NFCORE_PIPELINE

Defined in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:11

Keywords: utility, pipeline, initialise, version

Subworkflow with utility functions specific to the nf-core pipeline template

Inputs

Name	Description
`nextflow_cli_args`	Nextflow CLI positional arguments

Outputs

Name	Description
`success`	Dummy output to indicate success

Authors: @adamrtalbot Maintainers: @adamrtalbot, @maxulysse

UTILS_NEXTFLOW_PIPELINE

Defined in subworkflows/nf-core/utils_nextflow_pipeline/main.nf:11

Keywords: utility, pipeline, initialise, version

Subworkflow with functionality that may be useful for any Nextflow pipeline

Inputs

Name	Description
`print_version`	Print the version of the pipeline and exit
`dump_parameters`	Dump the parameters of the pipeline to a JSON file
`output_directory`	Path to output dir to write JSON file to.
`check_conda_channel`	Check if the conda channel priority is correct.

Outputs

Name	Description
`dummy_emit`	Dummy emit to make nf-core subworkflows lint happy

Authors: @adamrtalbot, @drpatelh Maintainers: @adamrtalbot, @drpatelh, @maxulysse

VCF_ANNOTATE_SNPEFF

Defined in subworkflows/nf-core/vcf_annotate_snpeff/main.nf:8

Keywords: vcf, annotation, snpeff

Perform annotation with snpEff and bgzip + tabix index the resulting VCF file

Components

This workflow uses the following modules/subworkflows:

snpeff
snpeff/snpeff
tabix/bgziptabix

Inputs

Name	Description
`ch_vcf`	vcf file Structure: [ val(meta), path(vcf) ]
`val_snpeff_db`	db version to use
`ch_snpeff_cache`	path to root cache folder for snpEff (optional) Structure: [ path(cache) ]

Outputs

Name	Description
`vcf_tbi`	Compressed vcf file + tabix index Structure: [ val(meta), path(vcf), path(tbi) ]
`reports`	html reports Structure: [ path(html) ]
`summary`	html reports Structure: [ path(csv) ]
`genes_txt`	html reports Structure: [ path(txt) ]
`versions`	Files containing software versions Structure: [ path(versions.yml) ]

Authors: @maxulysse Maintainers: @maxulysse

UTILS_NFSCHEMA_PLUGIN

Defined in subworkflows/nf-core/utils_nfschema_plugin/main.nf:9

Keywords: validation, JSON schema, plugin, parameters, summary

Run nf-schema to validate parameters and create a summary of changed parameters

Inputs

Name	Description
`input_workflow`	The workflow object of the used pipeline. This object contains meta data used to create the params summary log
`validate_params`	Validate the parameters and error if invalid.
`parameters_schema`	Path to the parameters JSON schema. This has to be the same as the schema given to the `validation.parametersSchema` config option. When this input is empty it will automatically use the configured schema or "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way for meta pipelines.

Outputs

Name	Description
`dummy_emit`	Dummy emit to make nf-core subworkflows lint happy

Authors: @nvnieuwk Maintainers: @nvnieuwk

VCF_ANNOTATE_ENSEMBLVEP

Defined in subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf:8

Keywords: vcf, annotation, ensemblvep

Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file

Components

This workflow uses the following modules/subworkflows:

ensemblvep/vep
tabix/tabix

Inputs

Name	Description
`ch_vcf`	vcf file to annotate Structure: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optional)] ]
`ch_fasta`	Reference genome fasta file (optional) Structure: [ val(meta2), path(fasta) ]
`val_genome`	genome to use
`val_species`	species to use
`val_cache_version`	cache version to use
`ch_cache`	the root cache folder for ensemblvep (optional) Structure: [ val(meta3), path(cache) ]
`ch_extra_files`	any extra files needed by plugins for ensemblvep (optional) Structure: [ path(file1), path(file2)... ]

Outputs

Name	Description
`vcf_tbi`	Compressed vcf file + tabix index Structure: [ val(meta), path(vcf), path(tbi) ]
`json`	json file Structure: [ val(meta), path(json) ]
`tab`	tab file Structure: [ val(meta), path(tab) ]
`reports`	html reports
`versions`	File containing software versions

Authors: @maxulysse, @matthdsm, @nvnieuwk Maintainers: @maxulysse, @matthdsm, @nvnieuwk

BAM_VARIANT_CALLING_SOMATIC_MUTECT2

Defined in subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf:17

Keywords: gatk4, mutect2, learnreadorientationmodel, getpileupsummaries, calculatecontamination, filtermutectcalls, variant_calling, tumor_only, filtered_vcf

Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode. f1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors. Run the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.

Components

This workflow uses the following modules/subworkflows:

gatk4/mutect2
gatk4/learnreadorientationmodel
gatk4/getpileupsummaries
gatk4/calculatecontamination
gatk4/filtermutectcalls

Inputs

Name	Description
`meta`	Groovy Map containing sample information e.g. [ id:'test' ]
`input`	list containing the tumor and normal BAM files, in that order, also able to take CRAM as an input
`input_index`	list containing the tumor and normal BAM file indexes, in that order, also able to take CRAM index as an input
`which_norm`	optional list of sample headers contained in the normal sample input file.
`fasta`	The reference fasta file
`fai`	Index of reference fasta file
`dict`	GATK sequence dictionary
`germline_resource`	Population vcf of germline sequencing, containing allele fractions.
`germline_resource_tbi`	Index file for the germline resource.
`panel_of_normals`	vcf file to be used as a panel of normals.
`panel_of_normals_tbi`	Index for the panel of normals.
`interval_file`	File containing intervals.

Outputs

Name	Description
`versions`	File containing software versions
`mutect2_vcf`	Compressed vcf file to be used for variant_calling.
`mutect2_tbi`	Indexes of the mutect2_vcf file
`mutect2_stats`	Stats files for the mutect2 vcf
`mutect2_f1r2`	file containing information to be passed to LearnReadOrientationModel.
`artifact_priors`	file containing artifact-priors to be used by filtermutectcalls.
`pileup_table_tumor`	File containing the tumor pileup summary table, kept separate as calculatecontamination needs them individually specified.
`pileup_table_normal`	File containing the normal pileup summary table, kept separate as calculatecontamination needs them individually specified.
`contamination_table`	File containing the contamination table.
`segmentation_table`	Output table containing segmentation of tumor minor allele fractions.
`filtered_vcf`	file containing filtered mutect2 calls.
`filtered_tbi`	tbi file that pairs with filtered vcf.
`filtered_stats`	file containing statistics of the filtermutectcalls run.

Authors: @GCJMackenzie

SAMPLESHEET_TO_CHANNEL

Defined in subworkflows/local/samplesheet_to_channel/main.nf:3

Inputs

Name	Description
`ch_from_samplesheet`	-
`aligner`	-
`ascat_alleles`	-
`ascat_loci`	-
`ascat_loci_gc`	-
`ascat_loci_rt`	-
`bcftools_annotations`	-
`bcftools_annotations_tbi`	-
`bcftools_columns`	-
`bcftools_header_lines`	-
`build_only_index`	-
`dbsnp`	-
`fasta`	-
`germline_resource`	-
`intervals`	-
`joint_germline`	-
`joint_mutect2`	-
`known_indels`	-
`known_snps`	-
`no_intervals`	-
`pon`	-
`sentieon_dnascope_emit_mode`	-
`sentieon_haplotyper_emit_mode`	-
`seq_center`	-
`seq_platform`	-
`skip_tools`	-
`snpeff_cache`	-
`snpeff_db`	-
`step`	-
`tools`	-
`umi_length`	-
`umi_location`	-
`umi_in_read_header`	-
`umi_read_structure`	-
`wes`	-

Outputs

Name	Description
`?`	-

CHANNEL_VARIANT_CALLING_CREATE_CSV

Defined in subworkflows/local/channel_variant_calling_create_csv/main.nf:5

Inputs

Name	Description
`vcf_to_annotate`	-
`outdir`	-

Outputs

Name	Description
`<none>`	-

BAM_VARIANT_CALLING_TUMOR_ONLY_LOFREQ

Defined in subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf:4

Inputs

Name	Description
`input`	-
`fasta`	-
`fai`	-
`intervals`	-
`dict`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2

Defined in subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf:16

Keywords: gatk4, mutect2, getpileupsummaries, calculatecontamination, filtermutectcalls, variant_calling, tumor_only, filtered_vcf

Perform variant calling on a single tumor sample using mutect2 tumor only mode. Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.

Components

This workflow uses the following modules/subworkflows:

gatk4/mutect2
gatk4/getpileupsummaries
gatk4/calculatecontamination
gatk4/filtermutectcalls

Inputs

Name	Description
`meta`	Groovy Map containing sample information e.g. [ id:'test' ]
`input`	list containing one BAM file, also able to take CRAM as an input
`input_index`	list containing one BAM file indexe, also able to take CRAM index as an input
`fasta`	The reference fasta file
`fai`	Index of reference fasta file
`dict`	GATK sequence dictionary
`germline_resource`	Population vcf of germline sequencing, containing allele fractions.
`germline_resource_tbi`	Index file for the germline resource.
`panel_of_normals`	vcf file to be used as a panel of normals.
`panel_of_normals_tbi`	Index for the panel of normals.
`interval_file`	File containing intervals.

Outputs

Name	Description
`versions`	File containing software versions
`mutect2_vcf`	Compressed vcf file to be used for variant_calling.
`mutect2_tbi`	Indexes of the mutect2_vcf file
`mutect2_stats`	Stats files for the mutect2 vcf
`pileup_table`	File containing the pileup summary table.
`contamination_table`	File containing the contamination table.
`segmentation_table`	Output table containing segmentation of tumor minor allele fractions.
`filtered_vcf`	file containing filtered mutect2 calls.
`filtered_tbi`	tbi file that pairs with filtered vcf.
`filtered_stats`	file containing statistics of the filtermutectcalls run.

Authors: @GCJMackenzie

BAM_JOINT_CALLING_GERMLINE_SENTIEON

Defined in subworkflows/local/bam_joint_calling_germline_sentieon/main.nf:15

Inputs

Name	Description
`input`	-
`fasta`	-
`fai`	-
`dict`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dbsnp_vqsr`	-
`resource_indels_vcf`	-
`resource_indels_tbi`	-
`known_indels_vqsr`	-
`resource_snps_vcf`	-
`resource_snps_tbi`	-
`known_snps_vqsr`	-
`variant_caller`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

VCF_QC_BCFTOOLS_VCFTOOLS

Defined in subworkflows/local/vcf_qc_bcftools_vcftools/main.nf:6

Inputs

Name	Description
`vcf`	-
`target_bed`	-

Outputs

Name	Description
`bcftools_stats`	-
`vcftools_tstv_counts`	-
`vcftools_tstv_qual`	-
`vcftools_filter_summary`	-
`?`	-

BAM_VARIANT_CALLING_SENTIEON_DNASCOPE

Defined in subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf:11

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-
`dict`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dbsnp_vqsr`	-
`intervals`	-
`joint_germline`	-
`sentieon_dnascope_emit_mode`	-
`sentieon_dnascope_pcr_indel_model`	-
`sentieon_dnascope_model`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_SOMATIC_MUSE

Defined in subworkflows/local/bam_variant_calling_somatic_muse/main.nf:11

Inputs

Name	Description
`bam_normal`	-
`bam_tumor`	-
`fasta`	-
`dbsnp`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_FREEBAYES

Defined in subworkflows/local/bam_variant_calling_freebayes/main.nf:14

Inputs

Name	Description
`ch_cram`	-
`ch_dict`	-
`ch_fasta`	-
`ch_fasta_fai`	-
`ch_intervals`	-

Outputs

Name	Description
`vcf_unfiltered`	-
`vcf`	-
`tbi`	-
`?`	-

CHANNEL_BASERECALIBRATOR_CREATE_CSV

Defined in subworkflows/local/channel_baserecalibrator_create_csv/main.nf:5

Inputs

Name	Description
`cram_table_bqsr`	-
`tools`	-
`skip_tools`	-
`outdir`	-
`save_output_as_bam`	-

Outputs

Name	Description
`<none>`	-

BAM_VARIANT_CALLING_SOMATIC_MANTA

Defined in subworkflows/local/bam_variant_calling_somatic_manta/main.nf:9

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_TUMOR_ONLY_ALL

Defined in subworkflows/local/bam_variant_calling_tumor_only_all/main.nf:17

Inputs

Name	Description
`tools`	-
`bam`	-
`cram`	-
`bwa`	-
`cf_chrom_len`	-
`chr_files`	-
`cnvkit_reference`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`germline_resource`	-
`germline_resource_tbi`	-
`intervals`	-
`intervals_bed_gz_tbi`	-
`intervals_bed_combined`	-
`intervals_bed_gz_tbi_combined`	-
`mappability`	-
`msisensor2_models`	-
`panel_of_normals`	-
`panel_of_normals_tbi`	-
`joint_mutect2`	-
`wes`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

PREPARE_REFERENCE_CNVKIT

Defined in subworkflows/local/prepare_reference_cnvkit/main.nf:4

Inputs

Name	Description
`fasta`	-
`intervals_bed_combined`	-

Outputs

Name	Description
`cnvkit_reference`	-
`?`	-

CONCATENATE_GERMLINE_VCFS

Defined in subworkflows/local/vcf_concatenate_germline/main.nf:12

Inputs

Name	Description
`vcfs`	-

Outputs

Name	Description
`vcfs`	-
`tbis`	-
`?`	-

BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC

Defined in subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf:13

Inputs

Name	Description
`controlfreec_input`	-
`fasta`	-
`fasta_fai`	-
`dbsnp`	-
`dbsnp_tbi`	-
`chr_files`	-
`mappability`	-
`intervals_bed`	-

Outputs

Name	Description
`versions`	-

BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA

Defined in subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf:10

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_SOMATIC_ALL

Defined in subworkflows/local/bam_variant_calling_somatic_all/main.nf:21

Inputs

Name	Description
`tools`	-
`bam`	-
`cram`	-
`bwa`	-
`cf_chrom_len`	-
`chr_files`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`germline_resource`	-
`germline_resource_tbi`	-
`intervals`	-
`intervals_bed_gz_tbi`	-
`intervals_bed_combined`	-
`intervals_bed_gz_tbi_combined`	-
`mappability`	-
`msisensorpro_scan`	-
`panel_of_normals`	-
`panel_of_normals_tbi`	-
`allele_files`	-
`loci_files`	-
`gc_file`	-
`rt_file`	-
`joint_mutect2`	-
`wes`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

BAM_MARKDUPLICATES_SPARK

Defined in subworkflows/local/bam_markduplicates_spark/main.nf:12

Inputs

Name	Description
`bam`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals_bed_combined`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_APPLYBQSR_SPARK

Defined in subworkflows/local/bam_applybqsr_spark/main.nf:11

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`bam`	-
`cram`	-
`?`	-

BAM_VARIANT_CALLING_SOMATIC_STRELKA

Defined in subworkflows/local/bam_variant_calling_somatic_strelka/main.nf:11

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

CHANNEL_MARKDUPLICATES_CREATE_CSV

Defined in subworkflows/local/channel_markduplicates_create_csv/main.nf:5

Inputs

Name	Description
`cram_markduplicates`	-
`csv_subfolder`	-
`outdir`	-
`save_output_as_bam`	-

Outputs

Name	Description
`<none>`	-

BAM_VARIANT_CALLING_DEEPVARIANT

Defined in subworkflows/local/bam_variant_calling_deepvariant/main.nf:12

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-

VCF_VARLOCIRAPTOR_SINGLE

Defined in subworkflows/local/vcf_varlociraptor_single/main.nf:9

Inputs

Name	Description
`ch_cram`	-
`ch_fasta`	-
`ch_fasta_fai`	-
`ch_scenario`	-
`ch_vcf`	-
`val_num_chunks`	-
`val_sampletype`	-

Outputs

Name	Description
`vcf`	-
`tbi`	-
`versions`	-

CRAM_QC_MOSDEPTH_SAMTOOLS

Defined in subworkflows/local/cram_qc_mosdepth_samtools/main.nf:10

Inputs

Name	Description
`cram`	-
`fasta`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-

DOWNLOAD_CACHE_SNPEFF_VEP

Defined in subworkflows/local/download_cache_snpeff_vep/main.nf:14

Inputs

Name	Description
`ensemblvep_info`	-
`snpeff_info`	-

Outputs

Name	Description
`ensemblvep_cache`	-
`snpeff_cache`	-
`?`	-

FASTQ_PREPROCESS_GATK

Defined in subworkflows/local/fastq_preprocess_gatk/main.nf:52

Inputs

Name	Description
`input_fastq`	-
`input_sample`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`index_alignment`	-
`intervals_and_num_intervals`	-
`intervals_for_preprocessing`	-
`known_sites_indels`	-
`known_sites_indels_tbi`	-
`bbsplit_index`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_MERGE_INDEX_SAMTOOLS

Defined in subworkflows/local/bam_merge_index_samtools/main.nf:10

Inputs

Name	Description
`bam`	-

Outputs

Name	Description
`?`	-
`?`	-

FASTQ_PREPROCESS_PARABRICKS

Defined in subworkflows/local/fastq_preprocess_parabricks/main.nf:4

Inputs

Name	Description
`ch_reads`	-
`ch_fasta`	-
`ch_index`	-
`ch_interval_file`	-
`ch_known_sites`	-
`val_output_fmt`	-

Outputs

Name	Description
`cram`	-
`versions`	-
`reports`	-

VCF_VARIANT_FILTERING_GATK

Defined in subworkflows/local/vcf_variant_filtering_gatk/main.nf:4

Inputs

Name	Description
`vcf`	-
`fasta`	-
`fasta_fai`	-
`dict`	-
`intervals_bed_combined`	-
`known_sites`	-
`known_sites_tbi`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_CONVERT_SAMTOOLS

Defined in subworkflows/local/bam_convert_samtools/main.nf:14

Inputs

Name	Description
`input`	-
`fasta`	-
`fasta_fai`	-
`interleaved`	-

Outputs

Name	Description
`?`	-
`?`	-

BAM_SENTIEON_DEDUP

Defined in subworkflows/local/bam_sentieon_dedup/main.nf:7

Inputs

Name	Description
`bam`	-
`bai`	-
`fasta`	-
`fasta_fai`	-
`intervals_bed_combined`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_SOMATIC_TIDDIT

Defined in subworkflows/local/bam_variant_calling_somatic_tiddit/main.nf:11

Inputs

Name	Description
`cram_normal`	-
`cram_tumor`	-
`fasta`	-
`bwa`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

CHANNEL_ALIGN_CREATE_CSV

Defined in subworkflows/local/channel_align_create_csv/main.nf:5

Inputs

Name	Description
`bam_indexed`	-
`outdir`	-
`save_output_as_bam`	-

Outputs

Name	Description
`<none>`	-

BAM_MARKDUPLICATES

Defined in subworkflows/local/bam_markduplicates/main.nf:10

Inputs

Name	Description
`bam`	-
`fasta`	-
`fasta_fai`	-
`intervals_bed_combined`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

CRAM_MERGE_INDEX_SAMTOOLS

Defined in subworkflows/local/cram_merge_index_samtools/main.nf:10

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-

Outputs

Name	Description
`?`	-
`?`	-

ANNOTATION_CACHE_INITIALISATION

Defined in subworkflows/local/annotation_cache_initialisation/main.nf:11

Inputs

Name	Description
`snpeff_enabled`	-
`snpeff_cache`	-
`snpeff_db`	-
`vep_enabled`	-
`vep_cache`	-
`vep_species`	-
`vep_cache_version`	-
`vep_genome`	-
`vep_custom_args`	-
`help_message`	-

Outputs

Name	Description
`?`	-
`?`	-

BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER

Defined in subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf:11

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-
`dict`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dbsnp_vqsr`	-
`intervals`	-
`joint_germline`	-
`sentieon_haplotyper_emit_mode`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_SINGLE_TIDDIT

Defined in subworkflows/local/bam_variant_calling_single_tiddit/main.nf:10

Inputs

Name	Description
`cram`	-
`fasta`	-
`bwa`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_CNVKIT

Defined in subworkflows/local/bam_variant_calling_cnvkit/main.nf:12

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-
`targets`	-
`reference`	-

Outputs

Name	Description
`cnv_calls_raw`	-
`cnv_calls_export`	-
`?`	-

CRAM_SAMPLEQC

Defined in subworkflows/local/cram_sampleqc/main.nf:4

Inputs

Name	Description
`cram`	-
`ngscheckmate_bed`	-
`fasta`	-
`skip_baserecalibration`	-
`intervals_for_preprocessing`	-

Outputs

Name	Description
`corr_matrix`	-
`matched`	-
`all`	-
`vcf`	-
`pdf`	-
`?`	-
`?`	-

CONSENSUS

Defined in subworkflows/local/vcf_consensus/main.nf:8

Inputs

Name	Description
`vcfs`	-

Outputs

Name	Description
`versions`	-
`vcfs`	-
`tbis`	-

BAM_VARIANT_CALLING_INDEXCOV

Defined in subworkflows/local/bam_variant_calling_indexcov/main.nf:11

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-

Outputs

Name	Description
`out_indexcov`	-
`?`	-

FASTQ_CREATE_UMI_CONSENSUS_FGBIO

Defined in subworkflows/local/fastq_create_umi_consensus_fgbio/main.nf:16

Inputs

Name	Description
`reads`	-
`fasta`	-
`fai`	-
`map_index`	-
`groupreadsbyumi_strategy`	-

Outputs

Name	Description
`umibam`	-
`groupbam`	-
`consensusbam`	-
`versions`	-

BAM_VARIANT_CALLING_MPILEUP

Defined in subworkflows/local/bam_variant_calling_mpileup/main.nf:12

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_SINGLE_STRELKA

Defined in subworkflows/local/bam_variant_calling_single_strelka/main.nf:11

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

POST_VARIANTCALLING

Defined in subworkflows/local/post_variantcalling/main.nf:12

Inputs

Name	Description
`tools`	-
`cram_germline`	-
`germline_vcfs`	-
`germline_tbis`	-
`cram_tumor_only`	-
`tumor_only_vcfs`	-
`tumor_only_tbis`	-
`cram_somatic`	-
`somatic_vcfs`	-
`somatic_tbis`	-
`fasta`	-
`fai`	-
`concatenate_vcfs`	-
`filter_vcfs`	-
`snv_consensus_calling`	-
`normalize_vcfs`	-
`varlociraptor_chunk_size`	-
`varlociraptor_scenario_germline`	-
`varlociraptor_scenario_somatic`	-
`varlociraptor_scenario_tumor_only`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

VCF_VARLOCIRAPTOR_SOMATIC

Defined in subworkflows/local/vcf_varlociraptor_somatic/main.nf:15

Inputs

Name	Description
`ch_cram`	-
`ch_fasta`	-
`ch_fasta_fai`	-
`ch_scenario`	-
`ch_somatic_vcf`	-
`ch_germline_vcf`	-
`val_num_chunks`	-

Outputs

Name	Description
`vcf`	-
`tbi`	-
`versions`	-

BAM_VARIANT_CALLING_GERMLINE_MANTA

Defined in subworkflows/local/bam_variant_calling_germline_manta/main.nf:10

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

BAM_APPLYBQSR

Defined in subworkflows/local/bam_applybqsr/main.nf:11

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-

Outputs

Name	Description
`bam`	-
`cram`	-
`?`	-

BAM_VARIANT_CALLING_SOMATIC_TNSCOPE

Defined in subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf:9

Inputs

Name	Description
`input`	-
`fasta`	-
`fai`	-
`dict`	-
`germline_resource`	-
`germline_resource_tbi`	-
`panel_of_normals`	-
`panel_of_normals_tbi`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

NORMALIZE_VCFS

Defined in subworkflows/local/vcf_normalization/main.nf:10

Inputs

Name	Description
`vcfs`	-
`fasta`	-

Outputs

Name	Description
`vcfs`	-
`tbis`	-
`?`	-

BAM_VARIANT_CALLING_TUMOR_ONLY_TNSCOPE

Defined in subworkflows/local/bam_variant_calling_tumor_only_tnscope/main.nf:9

Keywords: gatk4, mutect2, getpileupsummaries, calculatecontamination, filtermutectcalls, variant_calling, tumor_only, filtered_vcf

Perform variant calling on a single tumor sample using mutect2 tumor only mode. Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.

Components

This workflow uses the following modules/subworkflows:

gatk4/mutect2
gatk4/getpileupsummaries
gatk4/calculatecontamination
gatk4/filtermutectcalls

Inputs

Name	Description
`meta`	Groovy Map containing sample information e.g. [ id:'test' ]
`input`	list containing one BAM file, also able to take CRAM as an input
`input_index`	list containing one BAM file indexe, also able to take CRAM index as an input
`fasta`	The reference fasta file
`fai`	Index of reference fasta file
`dict`	GATK sequence dictionary
`germline_resource`	Population vcf of germline sequencing, containing allele fractions.
`germline_resource_tbi`	Index file for the germline resource.
`panel_of_normals`	vcf file to be used as a panel of normals.
`panel_of_normals_tbi`	Index for the panel of normals.
`interval_file`	File containing intervals.

Outputs

Name	Description
`versions`	File containing software versions
`mutect2_vcf`	Compressed vcf file to be used for variant_calling.
`mutect2_tbi`	Indexes of the mutect2_vcf file
`mutect2_stats`	Stats files for the mutect2 vcf
`pileup_table`	File containing the pileup summary table.
`contamination_table`	File containing the contamination table.
`segmentation_table`	Output table containing segmentation of tumor minor allele fractions.
`filtered_vcf`	file containing filtered mutect2 calls.
`filtered_tbi`	tbi file that pairs with filtered vcf.
`filtered_stats`	file containing statistics of the filtermutectcalls run.

Authors: @GCJMackenzie

BAM_VARIANT_CALLING_HAPLOTYPECALLER

Defined in subworkflows/local/bam_variant_calling_haplotypecaller/main.nf:11

Inputs

Name	Description
`cram`	-
`fasta`	-
`fasta_fai`	-
`dict`	-
`dbsnp`	-
`dbsnp_tbi`	-
`intervals`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

PIPELINE_INITIALISATION

Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:26

Inputs

Name	Description
`version`	-
`validate_params`	-
`nextflow_cli_args`	-
`outdir`	-
`input`	-
`help`	-
`help_full`	-
`show_hidden`	-

Outputs

Name	Description
`samplesheet`	-
`?`	-

PIPELINE_COMPLETION

Defined in subworkflows/local/utils_nfcore_sarek_pipeline/main.nf:203

Inputs

Name	Description
`email`	-
`email_on_fail`	-
`plaintext_email`	-
`outdir`	-
`monochrome_logs`	-
`hook_url`	-
`multiqc_report`	-

Outputs

Name	Description
`<none>`	-

PREPARE_GENOME

Defined in subworkflows/local/prepare_genome/main.nf:22

Inputs

Name	Description
`ascat_alleles_in`	-
`ascat_loci_in`	-
`ascat_loci_gc_in`	-
`ascat_loci_rt_in`	-
`bbsplit_fasta_list_in`	-
`bbsplit_index_in`	-
`bcftools_annotations_in`	-
`bcftools_annotations_tbi_in`	-
`bwa_in`	-
`bwamem2_in`	-
`chr_dir_in`	-
`dbsnp_in`	-
`dbsnp_tbi_in`	-
`dict_in`	-
`dragmap_in`	-
`fasta_in`	-
`fasta_fai_in`	-
`germline_resource_in`	-
`germline_resource_tbi_in`	-
`known_indels_in`	-
`known_indels_tbi_in`	-
`known_snps_in`	-
`known_snps_tbi_in`	-
`msisensor2_models_in`	-
`msisensorpro_scan_in`	-
`pon_in`	-
`pon_tbi_in`	-
`aligner`	-
`step`	-
`tools`	-
`vep_include_fasta`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC

Defined in subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf:13

Inputs

Name	Description
`controlfreec_input`	-
`fasta`	-
`fasta_fai`	-
`dbsnp`	-
`dbsnp_tbi`	-
`chr_files`	-
`mappability`	-
`intervals_bed`	-

Outputs

Name	Description
`versions`	-

BAM_BASERECALIBRATOR_SPARK

Defined in subworkflows/local/bam_baserecalibrator_spark/main.nf:10

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-
`known_sites`	-
`known_sites_tbi`	-

Outputs

Name	Description
`?`	-
`?`	-

BAM_BASERECALIBRATOR

Defined in subworkflows/local/bam_baserecalibrator/main.nf:10

Inputs

Name	Description
`cram`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-
`known_sites`	-
`known_sites_tbi`	-

Outputs

Name	Description
`?`	-
`?`	-

BAM_JOINT_CALLING_GERMLINE_GATK

Defined in subworkflows/local/bam_joint_calling_germline_gatk/main.nf:17

Inputs

Name	Description
`input`	-
`fasta`	-
`fai`	-
`dict`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dbsnp_vqsr`	-
`resource_indels_vcf`	-
`resource_indels_tbi`	-
`known_indels_vqsr`	-
`resource_snps_vcf`	-
`resource_snps_tbi`	-
`known_snps_vqsr`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-

CHANNEL_APPLYBQSR_CREATE_CSV

Defined in subworkflows/local/channel_applybqsr_create_csv/main.nf:5

Inputs

Name	Description
`cram_recalibrated_index`	-
`outdir`	-
`save_output_as_bam`	-

Outputs

Name	Description
`<none>`	-

FASTQ_ALIGN

Defined in subworkflows/local/fastq_align/main.nf:12

Inputs

Name	Description
`reads`	-
`index`	-
`sort`	-
`fasta`	-
`fasta_fai`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_GERMLINE_ALL

Defined in subworkflows/local/bam_variant_calling_germline_all/main.nf:22

Inputs

Name	Description
`tools`	-
`skip_tools`	-
`bam`	-
`cram`	-
`bwa`	-
`cnvkit_reference`	-
`dbsnp`	-
`dbsnp_tbi`	-
`dbsnp_vqsr`	-
`dict`	-
`fasta`	-
`fasta_fai`	-
`intervals`	-
`intervals_bed_combined`	-
`intervals_bed_gz_tbi_combined`	-
`intervals_bed_combined_haplotypec`	-
`intervals_bed_gz_tbi`	-
`known_indels_vqsr`	-
`known_sites_indels`	-
`known_sites_indels_tbi`	-
`known_sites_snps`	-
`known_sites_snps_tbi`	-
`known_snps_vqsr`	-
`joint_germline`	-
`skip_haplotypecaller_filter`	-
`sentieon_haplotyper_emit_mode`	-
`sentieon_dnascope_emit_mode`	-
`sentieon_dnascope_pcr_indel_model`	-
`sentieon_dnascope_model`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

VCF_ANNOTATE_ALL

Defined in subworkflows/local/vcf_annotate_all/main.nf:10

Inputs

Name	Description
`vcf`	-
`fasta`	-
`tools`	-
`snpeff_db`	-
`snpeff_cache`	-
`vep_genome`	-
`vep_species`	-
`vep_cache_version`	-
`vep_cache`	-
`vep_extra_files`	-
`bcftools_annotations`	-
`bcftools_annotations_index`	-
`bcftools_columns`	-
`bcftools_header_lines`	-

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

BAM_VARIANT_CALLING_SOMATIC_ASCAT

Defined in subworkflows/local/bam_variant_calling_somatic_ascat/main.nf:9

Inputs

Name	Description
`cram_pair`	-
`allele_files`	-
`loci_files`	-
`intervals_bed`	-
`fasta`	-
`gc_file`	-
`rt_file`	-

Outputs

Name	Description
`versions`	-

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:27:10 UTC.

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Workflows

Contents

NFCORE_SAREK

Inputs

Outputs

(entry)

SAREK

Inputs

Outputs

BAM_NGSCHECKMATE

Components

Inputs

Outputs

UTILS_NFCORE_PIPELINE

Inputs

Outputs

UTILS_NEXTFLOW_PIPELINE

Inputs

Outputs

VCF_ANNOTATE_SNPEFF

Components

Inputs

Outputs

UTILS_NFSCHEMA_PLUGIN

Inputs

Outputs

VCF_ANNOTATE_ENSEMBLVEP

Components

Inputs

Outputs

BAM_VARIANT_CALLING_SOMATIC_MUTECT2

Components

Inputs

Outputs

SAMPLESHEET_TO_CHANNEL

Inputs

Outputs

CHANNEL_VARIANT_CALLING_CREATE_CSV

Inputs

Outputs

BAM_VARIANT_CALLING_TUMOR_ONLY_LOFREQ

Inputs

Outputs

BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2

Components

Inputs

Outputs

BAM_JOINT_CALLING_GERMLINE_SENTIEON

Inputs

Outputs

VCF_QC_BCFTOOLS_VCFTOOLS

Inputs

Outputs

BAM_VARIANT_CALLING_SENTIEON_DNASCOPE

Inputs

Outputs

BAM_VARIANT_CALLING_SOMATIC_MUSE

Inputs

Outputs

BAM_VARIANT_CALLING_FREEBAYES

Inputs

Outputs

CHANNEL_BASERECALIBRATOR_CREATE_CSV

Inputs

Outputs

BAM_VARIANT_CALLING_SOMATIC_MANTA

Inputs

Outputs

BAM_VARIANT_CALLING_TUMOR_ONLY_ALL

Inputs

Outputs

PREPARE_REFERENCE_CNVKIT

Inputs

Outputs

CONCATENATE_GERMLINE_VCFS

Inputs

Outputs

BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC

Inputs

Outputs

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-

Name	Description
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-
`?`	-