FASTQC-FASTQSCREEN (✓ PRODUCTION)

Version: 1.0.0 Tags: Fastq / Quality control / Flamingo / Automated

This is the fully automated pipeline for quality assessment on Flamingo. No config, no design, no time wasted.

« A good pipeline has no documentation » Someone at BiGR

Pipeline dependencies

This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.

Conda:

  • conda-forge::python ==3.9.2

  • conda-forge::git ==2.30.2

  • conda-forge::jinja2 ==2.11.3

  • conda-forge::pygraphviz ==1.7

  • conda-forge::flask ==1.1.2

  • conda-forge::pandas ==1.2.3

  • conda-forge::zlib ==1.2.11

  • conda-forge::openssl ==1.1.1k

  • conda-forge::networkx ==2.5.1

  • bioconda::snakemake ==6.1.1

  • conda-forge::black ==20.8b1

  • conda-forge::singularity ==3.7.1

  • conda-forge::mamba ==0.9.2

Additionally, the following prerequisites are non-optional:

  • None. Everything is on Flamingo already.

Input files

Please find below the list of required input files:

  • Several paried Fastq files.

Output files

Please find below the list of expected output files:

  • MultiQC report

Notes

This pipeline handles iRODS copies.

Fastp -> Salmon -> MultiQC.

Installation

While installing the workflow, you may run the following commands (order matters):

Case

Command line

none

 
# No installation needed.

Testing

In order to test the pipeline, you may try the following commands:

Case

Command line

quick-test

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/fastqc_multiqc/test.sh

verbose-test

 
bash -x /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/fastqc_multiqc/test.sh

Preparation

In order to prepare a run, you may try the following commands:

Case

Command line

none

 
# No preparation, everything is available.

Execution

In order to execute the pipeline, you may run the following commands:

Case

Command line(s)

hg19

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/fastqc_multiqc/run.sh hg19

hg38

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/fastqc_multiqc/run.sh hg38