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Workflows

Workflows

This page documents all workflows in the pipeline.

Contents

(entry) (entry point)
minimap_pipeline
kraken_pipeline
run_common
run_amr

(entry)

Entry workflow

Defined in main.nf:27

minimap_pipeline

Defined in subworkflows/minimap_pipeline.nf:228

Inputs

Name	Description
`samples`	-
`reference`	-
`ref2taxid`	-
`taxonomy`	-
`taxonomic_rank`	-
`common_minimap2_opts`	-
`output_igv`	-

Outputs

Name	Description
`abundance_table`	-
`lineages`	-
`alignment_reports`	-
`metadata_after_taxonomy`	-

kraken_pipeline

Defined in subworkflows/kraken_pipeline.nf:157

Inputs

Name	Description
`samples`	-
`taxonomy`	-
`database`	-
`bracken_length`	-
`taxonomic_rank`	-

Outputs

Name	Description
`abundance_table`	-
`lineages`	-
`metadata_after_taxonomy`	-

run_common

Defined in subworkflows/common_pipeline.nf:65

Inputs

Name	Description
`samples`	-
`host_reference`	-
`common_minimap2_opts`	-

Outputs

Name	Description
`?`	-

run_amr

Defined in modules/local/amr.nf:44

Inputs

Name	Description
`input`	-
`amr_db`	-
`amr_minid`	-
`amr_mincov`	-

Outputs

Name	Description
`reports`	-

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