Galaxy | Published Workflow | GBS722 VACV-WR 125k - sample BWA to ref in hist / UAB

Published Workflows | curtish | 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.

Step	Annotation
Step 1: Input dataset input select at runtime	Ref FASTA
Step 2: Input dataset input select at runtime	FASTQsanger FWD
Step 3: Input dataset input select at runtime	FASTQsanger REV
Step 4: Input dataset input select at runtime	FASTQC Contamination List
Step 5: Map with BWA for Illumina Will you select a reference genome from your history or use a built-in index? Use one from the history Select a reference from history Output dataset 'output' from step 1 Is this library mate-paired? Paired-end Forward FASTQ file Output dataset 'output' from step 2 Reverse FASTQ file Output dataset 'output' from step 3 BWA settings to use Commonly Used Suppress the header in the output SAM file False
Step 6: Unknown Tool with id 'fastqc_demo'
Step 7: Unknown Tool with id 'fastqc_demo'
Step 8: SAM-to-BAM Choose the source for the reference genome Use a genome from the history SAM file to convert Output dataset 'output' from step 5 Using reference file Output dataset 'output' from step 1
Step 9: Unknown Tool with id 'sam_mpileup_view'
Step 10: Flagstat BAM File to report statistics of Output dataset 'output1' from step 8
Step 11: Unknown Tool with id 'snpEff_demo'