Reference guide

Use of minute command-line interface

minute <command> <options> <snakemake_specific_options>

command can be one of:

• init. Initializes a minute run creating the basic file structure and template configurations.
• download. Downloads FASTQ files from SRA.
• run. Runs the workflow.

General options

-h, --help Show help and exit.

--version Show version number and exit.

minute commands

init

Initialize a minute run. Parameters:

Positional

first. Path to the target directory where minute will run.

Named

--reads Path to the directory where the FASTQ file pairs are located.

--barcodes Path to the barcodes.tsv file. If not provided, init will not create libraries.tsv, groups.tsv files. Requires --reads to be provided.

--input Prefix of the FASTQ file pair that corresponds to the Input sample. It must match a file pair in the path specified by --reads. Required if --barcodes is provded.

--config Path to a minute.yaml file to reuse. It will be copied into the target directory.

download

Download FASTQ files from the Sequence Read Archive (SRA). It will download files with SRR codes specified in the fourth column of libraries.tsv file.

Parameters: None.

run

Run an already configured minute experiment directory. This is a wrapped Snakemake call, and its parameters work as Snakemake parameters. For instance, for a minute dry run of the target full:

minute run --dry-run full

See Snakemake documentation for more details.

Alternative target rules

By default, minute run will run the final rule, which generates demultiplexed FASTQ file pairs, final BAM files and scaled bigWig files, plus unscaled (1x genome coverage RPGC) for comparison. Note that Input bigWig tracks are always unscaled.

Alternative to this are:

full. Includes computationally costly extra QC: deepTools fingerprint.

quick. Runs the default pipeline but reduces the amount of bigWig files produced. Only scaled bigWig files will be generated for treatments, and unscaled bigWig files will be generated for controls.

no_bigwigs. Runs demultiplexing and alignment, but no bigWig generation. This still produces full scaling information and MultiQC report, and it is very quick to run.

mapq_bigwigs. Produces extra bigWigs mapq.bw filtered by mapping quality. This requires a mapping_quality_bigwig parameter value higher than zero in the minute.yaml configuration.

pooled_only. Produces only the bigWigs for the pooled replicates.

pooled_only_minimal. Runs the default pipeline, but it only generates bigWig files for the pools present in groups.tsv, scaled for treatment libraries and unscaled for the controls.

no_bigwigs. Runs the default pipeline but skips the bigWig generation entirely. This is useful for a quick check on QC metrics, since the rest of the steps are significantly faster than bigWig generation.

no_scaling. Skips entirely the scaling statistics and bigWigs. Produces only unscaled bigWigs and a MultiQC report with only non-scaling QC metrics.