Workflow: Metagenomics workflow

Fetched 2024-04-25 22:33:06 GMT

Workflow pilon assembly polishing Steps: - BBmap (Read mapping to assembly) - Pilon

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Inputs

ID Type Title Doc
memory Integer (Optional) Maximum memory in MB

Maximum memory usage in megabytes
fixlist String (Optional) Pilon fix list

A comma-separated list of categories of issues to try to fix
threads Integer (Optional) number of threads

number of threads to use for computational processes
assembly File Assembly

Assembly in fasta format
identifier String identifier used

Identifier for this dataset used in this workflow
destination String (Optional) Output Destination

Optional Output destination used for cwl-prov reporting.
illumina_forward_reads File forward reads

forward sequence file locally
illumina_reverse_reads File reverse reads

reverse sequence file locally

Steps

ID Runs Label Doc
pilon
../pilon/pilon.cwl (CommandLineTool)
Pilon

\"https://github.com/broadinstitute/pilon Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection\"

bam_index
../samtools/samtools_index.cwl (CommandLineTool)
samtools index

samtools index - creates an index file for bam file
vcf_compress
../bash/pigz.cwl (CommandLineTool)
compress a file multithreaded with pigz
readmapping_pilon
../bbmap/bbmap.cwl (CommandLineTool)
BBMap

Read filtering using BBMap against a (contamination) reference genome

sam_to_sorted_bam
../samtools/sam_to_sorted-bam.cwl (CommandLineTool)
sam to sorted bam

samtools view -@ $2 -hu $1 | samtools sort -@ $2 -o $3.bam

expressiontool_bam_index
../samtools/expression_bam_index.cwl (ExpressionTool)

Creates an \"hybrid\" output with the index file as secondary file.

Adapted from: https://github.com/vetscience/Assemblosis/blob/master/Run/expressiontoolbam.cwl

LICENSE: BSD 3-Clause License

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Outputs

ID Type Label Doc
log File Pilon log

Pilon log
vcf File VCF file

Compressed VCF file containing the changes.
pilon_polished_assembly File Polished genome
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Permalink: https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_pilon_mapping.cwl