nf-params.yml

## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##     nf-core/seqqc 1.0dev
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##     This is an example parameter file to pass to the `-params-file` option
##     of nextflow run with the nf-core/seqqc pipeline.
##      
##     Uncomment lines with a single '#' if you want to pass the parameter to
##     the pipeline.
## -----------------------------------------------------------------------------

## =============================================================================
## Sequencing parameters
## =============================================================================

## -----------------------------------------------------------------------------
## mode
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# mode = "illumina"

## -----------------------------------------------------------------------------
## nanopore_summary_file
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# nanopore_summary_file = null

## -----------------------------------------------------------------------------
## nanopore_summary_file_id
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# nanopore_summary_file_id = null


## =============================================================================
## Assembly QC
## =============================================================================

## -----------------------------------------------------------------------------
## checkm_db
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# checkm_db = "\"null\""

## -----------------------------------------------------------------------------
## combine_quast
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# combine_quast = null

## -----------------------------------------------------------------------------
## busco_lineage
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# busco_lineage = "auto"

## -----------------------------------------------------------------------------
## busco_lineages_path
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# busco_lineages_path = null

## -----------------------------------------------------------------------------
## busco_config
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# busco_config = null

## -----------------------------------------------------------------------------
## skip_checkm
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_checkm = null

## -----------------------------------------------------------------------------
## skip_quast
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_quast = null

## -----------------------------------------------------------------------------
## skip_busco
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_busco = null

## -----------------------------------------------------------------------------
## reference_genome_fasta
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# reference_genome_fasta = null

## -----------------------------------------------------------------------------
## reference_genome_gff
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# reference_genome_gff = null

## -----------------------------------------------------------------------------
## skip_assembly_qc
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_assembly_qc = null

## -----------------------------------------------------------------------------
## skip_rmlst
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_rmlst = null


## =============================================================================
## Taxonomy QC options
## =============================================================================

## -----------------------------------------------------------------------------
## classifier
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# classifier = "kraken2"

## -----------------------------------------------------------------------------
## skip_combinekreports
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_combinekreports = null

## -----------------------------------------------------------------------------
## skip_kreport2krona
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_kreport2krona = null

## -----------------------------------------------------------------------------
## skip_bracken
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_bracken = null

## -----------------------------------------------------------------------------
## skip_kraken2
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_kraken2 = null

## -----------------------------------------------------------------------------
## skip_combinebrackenoutputs
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_combinebrackenoutputs = null

## -----------------------------------------------------------------------------
## skip_dehosting
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_dehosting = null

## -----------------------------------------------------------------------------
## kraken2_db
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# kraken2_db = null

## -----------------------------------------------------------------------------
## classified_reads
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# classified_reads = true

## -----------------------------------------------------------------------------
## unclassified_reads
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# unclassified_reads = true

## -----------------------------------------------------------------------------
## centrifuge_db
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# centrifuge_db = null

## -----------------------------------------------------------------------------
## save_unaligned
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# save_unaligned = true

## -----------------------------------------------------------------------------
## save_aligned
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# save_aligned = true

## -----------------------------------------------------------------------------
## dehosting_aligner
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# dehosting_aligner = "minimap2"

## -----------------------------------------------------------------------------
## sam_format
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# sam_format = true

## -----------------------------------------------------------------------------
## bam_format
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# bam_format = true

## -----------------------------------------------------------------------------
## bwa_sort_bam
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# bwa_sort_bam = "sort"

## -----------------------------------------------------------------------------
## cigar_paf_format
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# cigar_paf_format = null

## -----------------------------------------------------------------------------
## cigar_bam
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# cigar_bam = null

## -----------------------------------------------------------------------------
## interleaved
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# interleaved = null

## -----------------------------------------------------------------------------
## host_genome
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# host_genome = null

## -----------------------------------------------------------------------------
## host_genome_id
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# host_genome_id = null

## -----------------------------------------------------------------------------
## skip_taxonomy_qc
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_taxonomy_qc = null


## =============================================================================
## Assembly options
## =============================================================================

## -----------------------------------------------------------------------------
## min_contig_len
## -----------------------------------------------------------------------------
##     Type: integer
## -----------------------------------------------------------------------------
# min_contig_len = 500

## -----------------------------------------------------------------------------
## min_contig_coverage
## -----------------------------------------------------------------------------
##     Type: integer
## -----------------------------------------------------------------------------
# min_contig_coverage = 2

## -----------------------------------------------------------------------------
## min_input_read_len
## -----------------------------------------------------------------------------
##     Type: integer
## -----------------------------------------------------------------------------
# min_input_read_len = 1000

## -----------------------------------------------------------------------------
## min_input_quality
## -----------------------------------------------------------------------------
##     Type: integer
## -----------------------------------------------------------------------------
# min_input_quality = 0

## -----------------------------------------------------------------------------
## racon_rounds
## -----------------------------------------------------------------------------
##     Type: integer
## -----------------------------------------------------------------------------
# racon_rounds = 1

## -----------------------------------------------------------------------------
## medaka_rounds
## -----------------------------------------------------------------------------
##     Type: integer
## -----------------------------------------------------------------------------
# medaka_rounds = 0

## -----------------------------------------------------------------------------
## medaka_model
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# medaka_model = "r941_min_fast_g507"

## -----------------------------------------------------------------------------
## sr_assembler
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# sr_assembler = "skesa"

## -----------------------------------------------------------------------------
## skip_assembly
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_assembly = null

## -----------------------------------------------------------------------------
## assembly_genomesize
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# assembly_genomesize = "\"''\""


## =============================================================================
## Raw Reads QC options
## =============================================================================

## -----------------------------------------------------------------------------
## adapter_fasta
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# adapter_fasta = null

## -----------------------------------------------------------------------------
## skip_subsampling
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_subsampling = null

## -----------------------------------------------------------------------------
## skip_confindr
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_confindr = null

## -----------------------------------------------------------------------------
## save_merged
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# save_merged = true

## -----------------------------------------------------------------------------
## trim_tool
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# trim_tool = "fastp"

## -----------------------------------------------------------------------------
## save_trimmed_fail
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# save_trimmed_fail = null

## -----------------------------------------------------------------------------
## depth_cut_off
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# depth_cut_off = null

## -----------------------------------------------------------------------------
## confindr_db
## -----------------------------------------------------------------------------
##     Type: string
## -----------------------------------------------------------------------------
# confindr_db = null

## -----------------------------------------------------------------------------
## skip_QC
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_QC = null

## -----------------------------------------------------------------------------
## skip_raw_qc
## -----------------------------------------------------------------------------
##     Type: boolean
## -----------------------------------------------------------------------------
# skip_raw_qc = null

## -----------------------------------------------------------------------------
## subsampling_genomesize
## -----------------------------------------------------------------------------
##     Type: integer
## -----------------------------------------------------------------------------
# subsampling_genomesize = null


## =============================================================================
## Input/output options
## =============================================================================
## Define where the pipeline should find input data and save output data.

## -----------------------------------------------------------------------------
## input
## -----------------------------------------------------------------------------
##     Path to comma-separated file containing information about the samples
##     in the experiment.
##     Type: string
## -----------------------------------------------------------------------------
# input = null

## -----------------------------------------------------------------------------
## outdir
## -----------------------------------------------------------------------------
##     The output directory where the results will be saved. You have to use
##     absolute paths to storage on Cloud infrastructure.
##     Type: string
## -----------------------------------------------------------------------------
# outdir = null

## -----------------------------------------------------------------------------
## email
## -----------------------------------------------------------------------------
##     Email address for completion summary.
##     Type: string
## -----------------------------------------------------------------------------
# email = null

## -----------------------------------------------------------------------------
## multiqc_title
## -----------------------------------------------------------------------------
##     MultiQC report title. Printed as page header, used for filename if not
##     otherwise specified.
##     Type: string
## -----------------------------------------------------------------------------
# multiqc_title = null


## =============================================================================
## Institutional config options
## =============================================================================
## Parameters used to describe centralised config profiles. These should not
## be edited.

## (6 hidden parameters are not shown)



## =============================================================================
## Max job request options
## =============================================================================
## Set the top limit for requested resources for any single job.

## (3 hidden parameters are not shown)



## =============================================================================
## Generic options
## =============================================================================
## Less common options for the pipeline, typically set in a config file.

## (13 hidden parameters are not shown)


## -----------------------------------------------------------------------------
## multiqc_methods_description
## -----------------------------------------------------------------------------
##     Custom MultiQC yaml file containing HTML including a methods
##     description.
##     Type: string
## -----------------------------------------------------------------------------
# multiqc_methods_description = null