CCS.BAM to FASTQ + QC (HiFi genome assembly stage 1)
Version 1

Workflow Type: Galaxy
Stable

Conversion of files from BAM to FASTQ, including FASTQC & CCS.BAM file quality control (QC) steps.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Inputs

ID Name Description Type
Input BAM Input BAM Input BAM file. For example, this could be sourced from a sequencing facility or from the Bioplatforms Australia data portal. n/a
inputFile inputFile runtime parameter for tool SamToFastq n/a
adapters adapters runtime parameter for tool FastQC n/a
contaminants contaminants runtime parameter for tool FastQC n/a
limits limits runtime parameter for tool FastQC n/a

Steps

ID Name Description
0 Input BAM Input BAM file. For example, this could be sourced from a sequencing facility or from the Bioplatforms Australia data portal.
1 SamToFastq toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2
2 Samtools flagstat toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3
3 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1

Outputs

ID Name Description Type
fq_single fq_single n/a
interleaved_fastq interleaved_fastq n/a
fq1 fq1 n/a
fq2 fq2 n/a
fq_u fq_u n/a
output1 output1 n/a
html_file html_file n/a
text_file text_file n/a

Version History

Version 1 (earliest) Created 21st Oct 2021 at 06:52 by Johan Gustafsson

Added/updated 1 files


Open master 21ba0d6
help Creators and Submitter
Creator
Submitter
Activity

Views: 1243   Downloads: 6

Created: 21st Oct 2021 at 06:52

Last updated: 9th Nov 2021 at 01:34

Last used: 7th Oct 2022 at 13:01

EDAM Properties
help Attributions

None

Total size: 10.5 KB
Powered by
(v.1.12.2)
Copyright © 2008 - 2022 The University of Manchester and HITS gGmbH

By continuing to use this site you agree to the use of cookies