Galaksio use case: Mouse ChIP-seq subworkflow

Annotation: This workflow aligns reads to the SacCer genome, filters aligned reads for MAPQ >20 and calculates the coverage. This workflow included in the parent workflow "Mouse version Parent Workflow ChIPSeq". Subworkflows cannot be altered directly and to change the output you need to edit the subworkflow in Galaxy, remove the subworkflow step in the parent workflow and then add it again (otherwise the parent workflow will run the original subworkflow version).

StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: Map with BWA
Use a built-in genome index
mm10
Single fastq
Output dataset 'output' from step 1
Do not set
Do not set
1.Simple Illumina mode
Use default job resource parameters
Step 3: Filter SAM or BAM, output SAM or BAM
Output dataset 'bam_output' from step 2
Include Header
20
no
Empty.
Empty.
select at runtime
False
Empty.
BAM (-b)
Step 4: bamCoverage
Output dataset 'output1' from step 3
25
Normalize coverage to 1x
mm9 (2150570000)
bigwig
Empty.
yes
1.0
Not available.
Empty.
False
A custom length, which will be applied to ALL reads.
150
False
False
1
Not available.
Not available.
0
0
False
Empty.
no
select at runtime
Use default job resource parameters