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# Run test sample through PEPPRO
name: test
metadata:
sample_annotation: "peppro_test.csv"
output_dir: "$HOME/peppro_test/"
pipeline_interfaces: "$HOME/peppro/pipeline_interface.yaml"
derived_columns: [read1]
data_sources:
R1: "$CODE/peppro/examples/data/{sample_name}_r1.fq.gz"
implied_columns:
organism:
human:
genome: hg38
prealignments: human_rDNA rCRSd
adapter: fastp # Default
dedup: seqkit # Default
trimmer: seqtk # Default
runon: pro # Default
umi_len: 8 # Default
max_len: 30 # Default
TSS_name: $HOME/genomes/hg38/hg38_TSS.tsv # Default. Pipeline checks corresponding genome folder without specifying.
CpA_name: $HOME/genomes/hg38/hg38_CpA.tsv # Default. Pipeline checks corresponding genome folder without specifying.
pre_name: $HOME/genomes/hg38/hg38_pre-mRNA.tsv # Default. Pipeline checks corresponding genome folder without specifying.
anno_name: $HOME/genomes/hg38/hg38_annotations.bed.gz # Default. Pipeline checks corresponding genome folder without specifying.
pipeline_args:
# peppro.py:
# "--sob": null # Default is FALSE. Pass flag to use seqOutBias for signal track generation and to incorporate mappability
# "--scale": null # Default is FALSE. Pass flag to scale seqOutBias signal tracks
# "--parts": 4 # Default. Split suffix tree generation into <4> parts. Higher number == less memory use.
# "--coverage": null # Default is FALSE. Pass flag to use coverage when producing library complexity plots.
# "--keep": null # Default is FALSE. Pass flag to keep prealignment BAM files.
# "--noFIFO": null # Default is FALSE. Pass flag to NOT use named pipes during prealignments.
# "--complexity": null # Default is TRUE. Pass flag to disable library complexity calculation. Faster.
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