Workflow Type: Common Workflow Language

Exome Alignment Workflow

Inputs

ID Name Description Type
fastq_files n/a List of paired-end input FASTQ files
  • File[]
reference_fasta n/a Compress FASTA files with the reference genome chromosomes
  • File
readgroup n/a Parsing header which should correlate to FASTQ files
  • string
sample_name n/a Sample name
  • string

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
  • File
Total size: 2.24 KB
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Activity

Views: 416   Downloads: 3

Created: 3rd Mar 2021 at 15:16

Last updated: 28th May 2021 at 13:44

Last used: 22nd Sep 2021 at 21:50

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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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