Workflow Type: Common Workflow Language
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Exome Alignment Workflow
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Inputs
ID | Name | Description | Type |
---|---|---|---|
fastq_files | n/a | List of paired-end input FASTQ files |
|
reference_fasta | n/a | Compress FASTA files with the reference genome chromosomes |
|
readgroup | n/a | Parsing header which should correlate to FASTQ files |
|
sample_name | n/a | Sample name |
|
Steps
ID | Name | Description |
---|---|---|
gunzip | n/a | n/a |
picard_dictionary | n/a | n/a |
cutadapt | n/a | n/a |
bwa_index | n/a | n/a |
samtools_faidx | n/a | n/a |
bwa_mem | n/a | n/a |
samtools_sort | n/a | n/a |
picard_markduplicates | n/a | n/a |
Outputs
ID | Name | Description | Type |
---|---|---|---|
sorted_bam | n/a | Sorted aligned BAM file |
|
Version History
Version 2 (latest) Created 28th May 2021 at 13:42 by Laura Rodriguez-Navas
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Version 1 (earliest) Created 3rd Mar 2021 at 15:16 by Laura Rodriguez-Navas
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Created: 3rd Mar 2021 at 15:16
Last updated: 28th May 2021 at 13:44
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