Published Workflows | curtish | GBS722 VACV-WR 125k - sample BWA to ref in hist

Galaxy Workflow ' GBS722 VACV-WR 125k - sample BWA to ref in hist'

Annotation: GBS722 class exercise: map sample to in-history reference using BWA, with QC and SNP calling and SNPeff. With sample_name variable.

StepAnnotation
Step 1: Input dataset
select at runtime
Ref FASTA
Step 2: Input dataset
select at runtime
FASTQsanger FWD
Step 3: Input dataset
select at runtime
FASTQsanger REV
Step 4: Input dataset
select at runtime
FASTQC Contamination List
Step 5: Map with BWA for Illumina
Use one from the history
Output dataset 'output' from step 1
Paired-end
Output dataset 'output' from step 2
Output dataset 'output' from step 3
Commonly Used
False
Step 6: Unknown Tool with id 'fastqc_demo'
Step 7: Unknown Tool with id 'fastqc_demo'
Step 8: SAM-to-BAM
Use a genome from the history
Output dataset 'output' from step 5
Output dataset 'output' from step 1
Step 9: Unknown Tool with id 'sam_mpileup_view'
Step 10: Flagstat
Output dataset 'output1' from step 8
Step 11: Unknown Tool with id 'snpEff_demo'