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Configuration .yaml files

The config.yaml and the cluster config.yaml files define the parameters for the run. The input config.yaml file must be in the inputs directory relative to the Snakefile and is the only required .yaml file. The config.yaml file can be specified from the command line using --configfile instead of making sure it is placed in the correct directory. The cluster config.yaml contains information specific to using Snakemake to submit jobs to the SLURM scheduler and can be found in the simple directory.

config.yaml

The config.yaml must contain the following fields:

Variable Description
output_dir Path to the output directory
idx_bt2 Path to the bowtie2 index
SAMPLES_TSV Path to the sample meta file in .tsv format
chrom_sizes Path to the chrom sizes .txt file
blacklist Path to the blacklist file .bed file
slop Slop size to use in bp
million_factor Millions factor to use, i.e. 1000000, 20000000, etc...
keepChr List of chromosomes to keep in the analysis
species Species of the experiments
maxatac_tfs List of TFs available from maxATAC to make predictions
flags Flags used for limiting the workflow steps performed

Example:

# Output directory
output_dir: /fs/project/PES0738/snakemake/runs/snakeatac_test_tobias

# Bowtie2 index
idx_bt2: /fs/project/PES0738/maxATAC_inputs/genome_inf/hg38/bowtie2_index/hg38

# STAR index: only required if TOBIAS analysis is performed
idx_star: /fs/project/PES0738/maxATAC_inputs/genome_inf/hg38/STAR_hg38_index

# Path to a TSV file with samples and their corresponding FASTQ file paths.
SAMPLES_TSV: '/fs/project/PES0738/snakemake/snakeATAC/inputs/sample.tsv'

# Path to chromosome sizes file
chrom_sizes: "/fs/project/PES0738/maxATAC_inputs/genome_inf/hg38.22XY.chrom.sizes"

# Path to blacklisted regions file
blacklist: "/fs/project/PES0738/maxATAC_inputs/genome_inf/hg38_maxatac_blacklist_V2.bed"

# Slop size to use around the Tn5 insertion sites
slop: 20

# What is the millions factor that you want to use to scale the read counts
million_factor: 20000000

# MACS2 species
species: "hs"

# List of chromosomes to limit the study to
keepChr: 'chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY'

maxatac_tfs:
  TCF7
  TCF12
  LEF1

# Analysis
flags:
  fastqc: True
  maxatac: True
  stranded: False
  tobias: False
  atacseqqc: False

Cluster config.yaml for use with SLURM

The cluster config.yaml is used to define default cluster configurations if you want to use Snakemake to submit jobs for you. If the rules do not have a resource limit described, they will default to these values when the job is submitted. This information is expanded on in the jdblischak/smk-simple-slur repo.

Example:

cluster:
  mkdir -p logs/{rule} &&
  sbatch
    --cpus-per-task={threads}
    --mem={resources.mem_mb}
    --job-name=smk-{rule}-{wildcards}
    --account={YOUR_ACCOUNT}
    --output=logs/{rule}/{rule}-{wildcards}-%j.out
    --time={resources.time}
    --parsable
default-resources:
  - time="12:00:00"
  - mem_mb=32000
restart-times: 3
max-jobs-per-second: 1
max-status-checks-per-second: 1
local-cores: 1
latency-wait: 60
jobs: 15
keep-going: True
rerun-incomplete: True
printshellcmds: True
scheduler: greedy
use-conda: True
cluster-status: status-sacct.sh