How to set pipeline parameters¶

Any parameter can be set via the CLI using two hyphens (--) followed by the parameter name and value. For example:

champagne run --output /data/$USER/champagne_project \
    --input assets/samplesheet_full_mm10.csv \
    --contrasts assets/contrasts_full_mm10.csv \
    --genome mm10 \
    --run_gem false \
    --run_chipseeker false \
    --run_qc true

Alternatively, you can create a YAML file with the parameters you want to set. This is useful for managing multiple parameters or for sharing configurations with others. Here's an example YAML file with some common parameters:

assets/params.yml

input: './assets/samplesheet_full_mm10.csv'
contrasts: './assets/contrasts_full_mm10.csv'
genome: mm10
run_gem: false
run_chipseeker: false
run_qc: true

You can then use these parameters with the -params-file option:

champagne run --output /data/$USER/champagne_project \
    -params-file assets/params.yml

View the full list of pipeline parameters below.

CCBR/CHAMPAGNE pipeline parameters¶

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

Input/output options¶

The most commonly used pipeline options

Parameter	Description	Type	Default	Required	Hidden
`input`	Path to comma-separated file containing information about the samples in the experiment. Help You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.	`string`		True
`contrasts`	Optional contrasts specification for differential analysis	`string`
`genome`	Reference genome (e.g. hg38, mm10). This can be a genome in conf/genomes.config, or see 'Custom genome options' to build a custom reference from a fasta & gtf file.	`string`		True
`outputDir`		`string`	${launchDir}/results		True
`tracedir`		`string`	${outputDir}/pipeline_info		True
`publish_dir_mode`		`string`	link

Custom genome options¶

Use these to build a custom reference genome not already listed in conf/genomes.config. For an example use-case, see conf/test.config.

Parameter	Description	Type
`genome_fasta`	Genome fasta file	`string`
`genes_gtf`	Genome gtf file	`string`
`blacklist`	Blacklisted sequences fasta file	`string`
`rename_contigs`	File with map to translate chromosome names (see assets/R64-1-1_ensembl2UCSC.txt as an example)	`string`
`index_dir`	Absolute path to directory containing pre-built reference genomes	`string`

General parameters¶

Parameter	Type	Default
`seq_center`	`string`
`read_length`	`integer`
`max_memory`	`string`	224 GB
`max_cpus`	`integer`	32
`max_time`	`string`	72 h
`align_min_quality`	`integer`	6
`min_fragment_length`	`integer`	200

Spike-in options¶

Options for experiments that use a spike-in genome

Parameter	Description	Type	Default
`spike_genome`	Optional spike-in genome (e.g. dmelr6.32, ecoli_k12). If null, spike-in normalization will not be performed.	`string`
`spike_norm_method`	Method to compute scaling factors for spike-in normalization. "guenther" uses a simple fraction of the reads aligning to the spike-in genome as described in https://doi.org/10.1016/j.celrep.2014.10.018. "delorenzi" uses deepTools multiBamSummary with --scalingFactors, which is similar to the method described in https://doi.org/10.1101/gr.168260.113.	`string`	guenther
`spike_deeptools_bin_size`	When spike_norm_method is delorenzi, this sets --binSize in deepTools multiBamSummary	`integer`	5000
`spike_deeptools_min_map_quality`	When spike_norm_method is delorenzi, this sets --minMappingQuality in deepTools multiBamSummary	`integer`	30

QC options¶

Parameter	Description	Type	Default
`fastq_screen_conf`		`string`
`fastq_screen_db_dir`		`string`
`deeptools_bin_size`		`integer`	25
`deeptools_smooth_length`		`integer`	75
`deeptools_normalize_using`	If using a spike-in genome, recommend setting this to "None"	`string`	RPGC
`deeptools_excluded_chroms`		`string`	chrM chrX chrY
`multiqc_config`		`string`	assets/multiqc_config.yaml
`multiqc_logo`		`string`	assets/ccbr_logo.png

Peak callers¶

Parameter	Type	Default
`macs_narrow_q`	`number`	0.01
`macs_broad_q`	`number`	0.01
`macs_broad_cutoff`	`number`	0.01
`gem_read_dists`	`string`	assets/gem/Read_Distribution_default.txt
`gem_fold`	`integer`	3
`gem_k_min`	`integer`	6
`gem_k_max`	`integer`	13
`sicer_species`	`string`

motifs¶

Parameter	Description	Type	Default	Required	Hidden
`homer_de_novo`		`boolean`	True
`homer_jaspar_db`		`string`	assets/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt

run control¶

Toggle various steps of the pipeline on/off

Parameter	Type	Default
`run_qc`	`boolean`	True
`run_deeptools`	`boolean`	True
`run_normalize_input`	`boolean`	True
`run_call_peaks`	`boolean`	True
`run_gem`	`boolean`	True
`run_sicer`	`boolean`	True
`run_macs_broad`	`boolean`	True
`run_macs_narrow`	`boolean`	True
`run_normalize_peaks`	`boolean`
`run_chipseeker`	`boolean`
`run_homer`	`boolean`	True
`run_meme`	`boolean`	True
`run_consensus_union`	`boolean`	True
`run_consensus_corces`	`boolean`	True

containers¶

Parameter	Type	Default
`containers_base`	`string`	nciccbr/ccbr_ubuntu_base_20.04:v6.1
`containers_deeptools`	`string`	nciccbr/ccbr_deeptools_3.5.3:v1
`containers_fastqc`	`string`	nciccbr/ccrgb_qctools:v4.0
`containers_fastq_screen`	`string`	nciccbr/ccbr_fastq_screen_0.14.1:v1.0
`containers_frip`	`string`	nciccbr/ccbr_frip:v1
`containers_gem`	`string`	nciccbr/ccbr_gem_3.4:v1
`containers_macs2`	`string`	nciccbr/ccbr_macs2_2.2.9.1:v1
`containers_multiqc`	`string`	nciccbr/ccbr_multiqc_1.15:v1
`containers_ngsqc`	`string`	nciccbr/ccbr_ngsqc_0.31:v1
`containers_phantom_peaks`	`string`	quay.io/biocontainers/phantompeakqualtools:1.2.2--hdfd78af_1
`containers_picard`	`string`	nciccbr/ccbr_picard_2.27.5:v1
`containers_preseq`	`string`	nciccbr/ccbr_preseq_v2.0:v1
`containers_r`	`string`	nciccbr/ccbr_r_4.3.0:v1
`containers_sicer`	`string`	nciccbr/ccbr_sicer2_1.0.3:v1

Other parameters¶

Parameter	Description	Type	Default	Required	Hidden
`diffbind_report`		`string`	assets/diffbind_report.Rmd		True