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Workflows

This page documents all workflows in the pipeline.

Contents

NFCORE_RNAVAR

Defined in main.nf:63

Inputs

Name Description
samplesheet -
align -

Outputs

Name Description
? -
? -

(entry)

Entry workflow

Defined in main.nf:211

RNAVAR

Defined in workflows/rnavar.nf:83

Main workflow for RNA variant calling analysis. This workflow performs end-to-end RNA-seq variant calling including:

  • Quality control with FastQC
  • Read alignment with STAR
  • Duplicate marking with Picard
  • Split N CIGAR reads for RNA-seq data
  • Base quality score recalibration (BQSR)
  • Variant calling with GATK HaplotypeCaller
  • Variant filtering
  • Variant annotation with SnpEff and VEP
  • HLA typing with seq2HLA (optional) The workflow supports multiple input types including FASTQ, BAM, CRAM, and VCF files.

Inputs

Name Description
input -
bcftools_annotations -
bcftools_annotations_tbi -
bcftools_columns -
bcftools_header_lines -
dbsnp -
dbsnp_tbi -
dict -
exon_bed -
fasta -
fasta_fai -
gtf -
known_sites -
known_sites_tbi -
star_index -
snpeff_cache -
snpeff_db -
vep_genome -
vep_species -
vep_cache_version -
vep_include_fasta -
vep_cache -
vep_extra_files -
seq_center -
seq_platform -
aligner -
bam_csi_index -
extract_umi -
generate_gvcf -
skip_multiqc -
skip_baserecalibration -
skip_intervallisttools -
skip_variantannotation -
skip_variantfiltration -
star_ignore_sjdbgtf -
tools -

Outputs

Name Description
? -
? -

BAM_STATS_SAMTOOLS

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

Keywords: statistics, counts, bam, sam, cram

Produces comprehensive statistics from SAM/BAM/CRAM file

Components

This workflow uses the following modules/subworkflows:

  • samtools/stats
  • samtools/idxstats
  • samtools/flagstat

Inputs

Name Description
ch_bam_bai The input channel containing the BAM/CRAM and it's index Structure: [ val(meta), path(bam), path(bai) ]
ch_fasta Reference genome fasta file Structure: [ path(fasta) ]

Outputs

Name Description
stats File containing samtools stats output Structure: [ val(meta), path(stats) ]
flagstat File containing samtools flagstat output Structure: [ val(meta), path(flagstat) ]
idxstats File containing samtools idxstats output Structure: [ val(meta), path(idxstats)]
versions Files containing software versions Structure: [ path(versions.yml) ]

Authors: @drpatelh Maintainers: @drpatelh

FASTQ_ALIGN_STAR

Defined in subworkflows/nf-core/fastq_align_star/main.nf:6

Keywords: align, fasta, genome, reference

Align reads to a reference genome using bowtie2 then sort with samtools

Components

This workflow uses the following modules/subworkflows:

  • star/align
  • samtools/sort
  • samtools/index
  • samtools/stats
  • samtools/idxstats
  • samtools/flagstat
  • bam_sort_stats_samtools

Inputs

Name Description
ch_reads List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. Structure: [ val(meta), [ path(reads) ] ]
ch_index STAR genome index
ch_gtf GTF file used to set the splice junctions with the --sjdbGTFfile flag
val_star_ignore_sjdbgtf If true the --sjdbGTFfile flag is set
val_seq_platform Sequencing platform to be added to the bam header using the --outSAMattrRGline flag
val_seq_center Sequencing center to be added to the bam header using the --outSAMattrRGline flag
ch_fasta Reference genome fasta file
ch_transcripts_fasta Optional reference genome fasta file

Outputs

Name Description
orig_bam Output BAM file containing read alignments Structure: [ val(meta), path(bam) ]
log_final STAR final log file Structure: [ val(meta), path(log_final) ]
log_out STAR log out file Structure: [ val(meta), path(log_out) ]
log_progress STAR log progress file Structure: [ val(meta), path(log_progress) ]
bam_sorted Sorted BAM file of read alignments (optional) Structure: [ val(meta), path(bam) ]
orig_bam_transcript Output BAM file of transcriptome alignment (optional) Structure: [ val(meta), path(bam) ]
fastq Unmapped FastQ files (optional) Structure: [ val(meta), path(fastq) ]
tab STAR output tab file(s) (optional) Structure: [ val(meta), path(tab) ]
bam BAM file ordered by samtools Structure: [ val(meta), path(bam) ]
bai BAI index of the ordered BAM file Structure: [ val(meta), path(bai) ]
stats File containing samtools stats output Structure: [ val(meta), path(stats) ]
flagstat File containing samtools flagstat output Structure: [ val(meta), path(flagstat) ]
idxstats File containing samtools idxstats output Structure: [ val(meta), path(idxstats) ]
bam_transcript Transcriptome-level BAM file ordered by samtools (optional) Structure: [ val(meta), path(bam) ]
bai_transcript Transcriptome-level BAI index of the ordered BAM file (optional) Structure: [ val(meta), path(bai) ]
stats_transcript Transcriptome-level file containing samtools stats output (optional) Structure: [ val(meta), path(stats) ]
flagstat_transcript Transcriptome-level file containing samtools flagstat output (optional) Structure: [ val(meta), path(flagstat) ]
idxstats_transcript Transcriptome-level file containing samtools idxstats output (optional) Structure: [ val(meta), path(idxstats) ]
versions File containing software versions

Authors: @JoseEspinosa Maintainers: @JoseEspinosa

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

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_MARKDUPLICATES_PICARD

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

Keywords: markduplicates, bam, sam, cram

Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats

Components

This workflow uses the following modules/subworkflows:

  • picard/markduplicates
  • samtools/index
  • samtools/stats
  • samtools/idxstats
  • samtools/flagstat
  • bam_stats_samtools

Inputs

Name Description
ch_reads Sequence reads in BAM/CRAM/SAM format Structure: [ val(meta), path(reads) ]
ch_fasta Reference genome fasta file required for CRAM input Structure: [ path(fasta) ]
ch_fasta Index of the reference genome fasta file Structure: [ path(fai) ]

Outputs

Name Description
bam processed BAM/SAM file Structure: [ val(meta), path(bam) ]
bai BAM/SAM samtools index Structure: [ val(meta), path(bai) ]
cram processed CRAM file Structure: [ val(meta), path(cram) ]
crai CRAM samtools index Structure: [ val(meta), path(crai) ]
csi CSI samtools index Structure: [ val(meta), path(csi) ]
stats File containing samtools stats output Structure: [ val(meta), path(stats) ]
flagstat File containing samtools flagstat output Structure: [ val(meta), path(flagstat) ]
idxstats File containing samtools idxstats output Structure: [ val(meta), path(idxstats) ]
versions Files containing software versions Structure: [ path(versions.yml) ]

Authors: @dmarron, @drpatelh Maintainers: @dmarron, @drpatelh

BAM_SORT_STATS_SAMTOOLS

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

Keywords: sort, bam, sam, cram

Sort SAM/BAM/CRAM file

Components

This workflow uses the following modules/subworkflows:

  • samtools/sort
  • samtools/index
  • samtools/stats
  • samtools/idxstats
  • samtools/flagstat
  • bam_stats_samtools

Inputs

Name Description
meta Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
bam BAM/CRAM/SAM file
fasta Reference genome fasta file

Outputs

Name Description
meta Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
bam Sorted BAM/CRAM/SAM file
bai BAM/CRAM/SAM index file
crai BAM/CRAM/SAM index file
stats File containing samtools stats output
flagstat File containing samtools flagstat output
idxstats File containing samtools idxstats output
versions File containing software versions

Authors: @drpatelh, @ewels Maintainers: @drpatelh, @ewels

PREPARE_ALIGNMENT

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

Inputs

Name Description
cram -
bam -

Outputs

Name Description
bam -
versions -

SPLITNCIGAR

Defined in subworkflows/local/splitncigar/main.nf:25

Split reads that contain N CIGAR operations for RNA-seq variant calling. This subworkflow handles the GATK SplitNCigarReads step which is essential for RNA-seq variant calling. It splits reads that span introns (N in CIGAR) and reassigns mapping qualities to meet GATK requirements. The workflow processes BAM files in parallel across genomic intervals, then merges and indexes the results for efficient downstream processing.

Inputs

Name Description
bam -
fasta -
fai -
dict -
intervals -

Outputs

Name Description
bam_bai -
versions -

RECALIBRATE

Defined in subworkflows/local/recalibrate/main.nf:27

Apply base quality score recalibration (BQSR) to BAM files. This subworkflow applies the BQSR model generated by GATK BaseRecalibrator to adjust base quality scores in BAM files. Recalibrated quality scores improve the accuracy of variant calling by correcting systematic errors in the original quality scores assigned by the sequencing machine. Optionally generates alignment statistics using samtools stats for QC.

Inputs

Name Description
skip_samtools -
bam -
dict -
fai -
fasta -

Outputs

Name Description
bam -
qc -
versions -

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 -

PIPELINE_INITIALISATION

Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:51

Initialize the nf-core/rnavar pipeline. Performs all setup tasks required before running the main workflow:

  • Display version information if requested
  • Validate parameters against the schema
  • Check Conda channel configuration
  • Parse and validate the input samplesheet
  • Generate parameter summary for logging

Inputs

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

Outputs

Name Description
samplesheet -
align -
versions -

PIPELINE_COMPLETION

Defined in subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf:198

Handle pipeline completion tasks. Executes cleanup and notification tasks when the pipeline finishes:

  • Send completion email with run summary
  • Generate completion summary to stdout
  • Send notifications to messaging platforms (Slack, Teams, etc.)
  • Log error messages for failed runs

Inputs

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

Outputs

Name Description
<none> -

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
? -
? -

PREPARE_GENOME

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

Inputs

Name Description
bcftools_annotations -
bcftools_annotations_tbi -
dbsnp -
dbsnp_tbi -
dict -
exon_bed -
fasta -
fasta_fai -
gff -
gtf -
known_indels -
known_indels_tbi -
star_index -
feature_type -
skip_exon_bed_check -
align -

Outputs

Name Description
bcfann -
bcfann_tbi -
dbsnp -
dbsnp_tbi -
dict -
exon_bed -
fasta -
fasta_fai -
gtf -
known_indels -
known_indels_tbi -
known_sites -
known_sites_tbi -
star_index -
versions -

VCF_ANNOTATE_ALL

Defined in subworkflows/local/vcf_annotate_all/main.nf:37

Annotate variants using multiple annotation tools. This subworkflow provides flexible variant annotation using one or more tools:

  • SnpEff: Functional annotation and effect prediction
  • VEP (Ensembl Variant Effect Predictor): Comprehensive variant annotation
  • BCFtools annotate: Add custom annotations from external files
  • Merge: Combined SnpEff + VEP annotation The tools to use are specified via the tools parameter as a comma-separated list (e.g., "snpeff,vep" or "merge").

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
? -
? -
? -
? -

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:23:12 UTC.