MultiQC Report

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If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.0.dev0

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

Report generated on 2020-02-18, 20:02 based on data in: /scratch/mk5636/nextflow_work_dir/dc/231b92ec5f69366f73ee84e44351f0

General Statistics

Showing ¹/₁ rows and ²/₃ columns.

Sample Name	Insert Size	Mean Insert Size	% Aligned
HT27VBGXC_2_no_human_sorted_dedup	198	200	0%

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Sort	Group	Column	Description	ID	Scale
\|\|	Picard	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	Picard	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None
\|\|	Picard	% Aligned	Percent of aligned reads	`PCT_PF_READS_ALIGNED`	None

Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

Insert Size

Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

Alignment Summary

Plase note that Picard's read counts are divided by two for paired-end data.

Cluster Flow

Cluster Flow is a simple and flexible bioinformatics pipeline tool.

Pipelines

Information about pipelines is parsed from *.run files.

Showing ¹/₁ rows and ¹/₁ columns.

Pipeline ID	# Starting Files
unknown	0

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		Cluster Flow	# Starting Files	Number of input files at start of pipeline run.	`num_starting_files`	None

Pipeline Steps: unknown (`None`)

#!/bin/bash
#SBATCH -D /scratch/mk5636/nextflow_work_dir/dc/231b92ec5f69366f73ee84e44351f0
#SBATCH -J nf-parseMetrics_(2)
#SBATCH -o /scratch/mk5636/nextflow_work_dir/dc/231b92ec5f69366f73ee84e44351f0/.command.log
#SBATCH --no-requeue
#SBATCH -c 10
#SBATCH -t 01:00:00
#SBATCH --mem 30720
# NEXTFLOW TASK: parseMetrics (2)
# task environment
# stage input files

Commands

Every Cluster Flow run will have many different commands. MultiQC splits these by whitespace, collects by the tool name and shows the first command found. Any terms not found in all subsequent calls are replaced with [variable] (typically input and ouput filenames). Each column is for one Cluster Flow run.

Showing ⁰/₀ rows and ⁰/₀ columns.

Tool

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Sort	Visible	Group	Column	Description	ID	Scale

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About MultiQC

General Statistics

General Statistics: Columns

Picard

Insert Size

Alignment Summary

Cluster Flow

Pipelines

Cluster Flow Pipelines: Columns

Pipeline Steps: unknown (None)

Commands

Cluster Flow Commands: Columns

v1.0.dev0

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Pipeline Steps: unknown (`None`)