Skip to content

Processes

This page documents all processes in the pipeline.

Contents

minimap

Defined in subworkflows/minimap_pipeline.nf:11

Inputs

Name Type Description
val(meta), path(concat_seqs), path(stats) tuple -

Outputs

Name Type Emit Description
val(meta) tuple - -

minimapTaxonomy

Defined in subworkflows/minimap_pipeline.nf:89

Inputs

Name Type Description
val(meta), path(assignments) tuple -

Outputs

Name Type Emit Description
val(meta) tuple - -

extractMinimap2Reads

Defined in subworkflows/minimap_pipeline.nf:141

Inputs

Name Type Description
val(meta), path("alignment.bam"), path("alignment.bai"), path("bamstats"), val(n_unmapped) tuple -

Outputs

Name Type Emit Description
val(meta) tuple - -

getAlignmentStats

Defined in subworkflows/minimap_pipeline.nf:181

Inputs

Name Type Description
val(meta), path("input.bam"), path("input.bam.bai"), path("bamstats") tuple -

Outputs

Name Type Emit Description
${meta.alias path - -

run_kraken2

Defined in subworkflows/kraken_pipeline.nf:8

Inputs

Name Type Description
val(meta), path("reads.fq.gz"), path(fastq_stats) tuple -

Outputs

Name Type Emit Description
val(meta) tuple - -

run_bracken

Defined in subworkflows/kraken_pipeline.nf:72

Inputs

Name Type Description
val(meta), path("kraken2.report"), path("kraken2.assignments.tsv") tuple -
bracken_length.txt path -

Outputs

Name Type Emit Description
val(meta) tuple - -

output_kraken2_read_assignments

Defined in subworkflows/kraken_pipeline.nf:129

Inputs

Name Type Description
val(meta) tuple -

Outputs

Name Type Emit Description
val(meta), path("*_lineages.kraken2.assignments.tsv") tuple - -

exclude_host_reads

Defined in subworkflows/common_pipeline.nf:1

Inputs

Name Type Description
val(meta), path(concat_seqs), path(fastcat_stats) tuple -

Outputs

Name Type Emit Description
val(meta), path("*.unmapped.fastq.gz"), path("stats_unmapped"), env(n_seqs_passed_host_depletion) tuple fastq -
val(meta), path("*.host.bam"), path("*.host.bam.bai") tuple host_bam -
val(meta), path("*.unmapped.bam"), path("*.unmapped.bam.bai") tuple no_host_bam -

fastcat

Defined in lib/ingress.nf:587

Inputs

Name Type Description
val(meta), path(input_src, stageAs: "input_src") tuple -

Outputs

Name Type Emit Description
val(meta), path("fastq_chunks/*.fastq.gz"), path("fastcat_stats") tuple - -

checkBamHeaders

Defined in lib/ingress.nf:650

Inputs

Name Type Description
val(meta), path("input_dir/reads*.bam") tuple -

Outputs

Name Type Emit Description
val(meta), path("input_dir/reads*.bam", includeInputs: true), env(IS_UNALIGNED), env(MIXED_HEADERS), env(IS_SORTED) tuple - -

validateIndex

Defined in lib/ingress.nf:672

Inputs

Name Type Description
val(meta), path("reads.bam"), path("reads.bam.bai") tuple -

Outputs

Name Type Emit Description
val(meta), path("reads.bam", includeInputs: true), path("reads.bam.bai", includeInputs: true), env(HAS_VALID_INDEX) tuple - -

mergeBams

Defined in lib/ingress.nf:698

Inputs

Name Type Description
val(meta), path("input_bams/reads*.bam") tuple -

Outputs

Name Type Emit Description
val(meta), path("reads.bam"), path("reads.bam.bai") tuple - -

catSortBams

Defined in lib/ingress.nf:715

Inputs

Name Type Description
val(meta), path("input_bams/reads*.bam") tuple -

Outputs

Name Type Emit Description
val(meta), path("reads.bam"), path("reads.bam.bai") tuple - -

sortBam

Defined in lib/ingress.nf:731

Inputs

Name Type Description
val(meta), path("reads.bam") tuple -

Outputs

Name Type Emit Description
val(meta), path("reads.sorted.bam"), path("reads.sorted.bam.bai") tuple - -

bamstats

Defined in lib/ingress.nf:746

Inputs

Name Type Description
val(meta), path("reads.bam"), path("reads.bam.bai") tuple -

Outputs

Name Type Emit Description
val(meta), path("reads.bam"), path("reads.bam.bai"), path("bamstats_results") tuple - -

move_or_compress_fq_file

Defined in lib/ingress.nf:792

Inputs

Name Type Description
val(meta), path(input) tuple -

Outputs

Name Type Emit Description
val(meta), path("seqs.fastq.gz") tuple - -

split_fq_file

Defined in lib/ingress.nf:818

Inputs

Name Type Description
val(meta), path(input) tuple -

Outputs

Name Type Emit Description
val(meta), path("fastq_chunks/*.fastq.gz") tuple - -

validate_sample_sheet

Defined in lib/ingress.nf:1219

Python script for validating a sample sheet. The script will write messages to STDOUT if the sample sheet is invalid. In case there are no issues, no message is emitted. The sample sheet will be published to the output dir.

Inputs

Name Type Description
sample_sheet.csv path -

Outputs

Name Type Emit Description
path("sample_sheet.csv") tuple - -

samtools_index

Defined in lib/ingress.nf:1238

Inputs

Name Type Description
val(meta), path("reads.bam") tuple -

Outputs

Name Type Emit Description
val(meta), path("reads.bam"), path("reads.bam.bai") tuple - -

getParams

Defined in lib/common.nf:3

Outputs

Name Type Emit Description
params.json path - -

configure_igv

Defined in lib/common.nf:19

Inputs

Name Type Description
file-names.txt path -

Outputs

Name Type Emit Description
igv.json path - -

abricate

Defined in modules/local/amr.nf:1

Inputs

Name Type Description
val(meta), path("input_reads.fastq.gz"), path("stats/") tuple -

Outputs

Name Type Emit Description
val(meta) tuple - -

abricate_json

Defined in modules/local/amr.nf:24

Inputs

Name Type Description
val(meta) tuple -

Outputs

Name Type Emit Description
val(meta) tuple - -

filter_references

Defined in modules/local/igv_related.nf:6

Inputs

Name Type Description
bam_flagstats/* path -

Outputs

Name Type Emit Description
path("reduced_reference.fasta.gz"), path("reduced_reference.fasta.gz.fai"), path("reduced_reference.fasta.gz.gzi") tuple - -

abricateVersion

Defined in modules/local/common.nf:3

Inputs

Name Type Description
input_versions.txt path -

Outputs

Name Type Emit Description
versions.txt path - -

getVersions

Defined in modules/local/common.nf:19

Outputs

Name Type Emit Description
versions.txt path - -

getVersionsCommon

Defined in modules/local/common.nf:41

Inputs

Name Type Description
versions.txt path -

Outputs

Name Type Emit Description
versions_all.txt path - -

createAbundanceTables

Defined in modules/local/common.nf:62

Inputs

Name Type Description
lineages/* path -

Outputs

Name Type Emit Description
abundance_table_*.tsv path abundance_tsv -

publishReads

Defined in modules/local/common.nf:84

Inputs

Name Type Description
val(meta), path("reads.fq.gz"), path("ids.txt") tuple -

Outputs

Name Type Emit Description
${meta.alias path - -

publish

Defined in modules/local/common.nf:104

Inputs

Name Type Description
path(fname), val(dirname) tuple -

Outputs

Name Type Emit Description
fname path - -

makeReport

Defined in modules/local/common.nf:124

Inputs

Name Type Description
abundance_table.tsv path -
alignment_stats/* path -
lineages/* path -
versions/* path -
params.json path -
amr/* path -

Outputs

Name Type Emit Description
${report_name path - -

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:27:31 UTC.