Stable
Virus genome assembly with Unicycler and Spades,
The 2 assemblers works in parallel. The graph visualization is made with Bandage.
workflow git repository : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl
Based on https://github.com/galaxyproject/SARS-CoV-2/blob/master/genomics/2-Assembly/as_wf.png
Inputs
ID | Name | Description | Type |
---|---|---|---|
fastq_file_type | n/a | Paired and single end data | {"type"=>"enum", "symbols"=>["paired", "single"]} |
mode | n/a | Bridging mode, values: conservative (smaller contigs, lower misassembly) normal (moderate contig size and misassembly rate) bold (longest contigs, higher misassembly rate) | {"type"=>"enum", "symbols"=>["conservative", "normal", "bold"]} |
fastq1_type | n/a | Type of the First set of reads. Only when fastq_file_type = single or paired | {"type"=>"enum", "symbols"=>["fastqsanger", "fastqsanger.gz"]} |
fastq1 | n/a | First set of reads with forward reads. Only when fastq_file_type = single or paired | File |
fastq2_type | n/a | Type of the Second set of reads. Only when fastq_file_type=paired | {"type"=>"enum", "symbols"=>["fastqsanger", "fastqsanger.gz"]} (Optional) |
fastq2 | n/a | Second set of reads with reverse reads. Only when fastq_file_type=paired | File? |
libraries_metadata | n/a | reads library metadata related to libraries_fwd_rev and libraries_mono inputs lib_index(id) must match | {"type"=>"array", "items"=>{"type"=>"record", "fields"=>[{"name"=>"lib_index", "type"=>"int?"}, {"name"=>"orientation", "type"=>"string?"}, {"name"=>"lib_type", "type"=>"string?"}]}} |
libraries_fwd_rev | n/a | reads file orientation must be a value in ff, fr, rf K-mer choices can be chosen by SPAdes instead of being entered manually | {"type"=>"array", "items"=>{"type"=>"record", "fields"=>[{"name"=>"lib_index", "type"=>"int?"}, {"name"=>"fwd_reads", "type"=>"File?"}, {"name"=>"rev_reads", "type"=>"File?"}]}} |
libraries_mono | n/a | reads file file_type value must be in : interleaved, merged, unpaired | {"type"=>"array", "items"=>{"type"=>"record", "fields"=>[{"name"=>"lib_index", "type"=>"int?"}, {"name"=>"file_type", "type"=>"string?"}, {"name"=>"reads", "type"=>"File?"}]}} |
pacbio_reads | n/a | n/a | {"type"=>"array", "items"=>"File"} (Optional) |
nanopore_reads | n/a | n/a | {"type"=>"array", "items"=>"File"} (Optional) |
sanger_reads | n/a | n/a | {"type"=>"array", "items"=>"File"} (Optional) |
trusted_contigs | n/a | n/a | {"type"=>"array", "items"=>"File"} (Optional) |
untrusted_contigs | n/a | n/a | {"type"=>"array", "items"=>"File"} (Optional) |
auto_kmer_choice | n/a | Automatically choose k-mer values. K-mer choices can be chosen by SPAdes instead of being entered manually | boolean |
kmers | n/a | K-mers to use, separated by commas. Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55 | string |
cov_state | n/a | Coverage cutoff ( 'auto', or 'off', or 'value'). auto if null when cov_state=value (User Specific) , cov_cutoff must be provided | {"type"=>"enum", "symbols"=>[false, "value", "auto"]} (Optional) |
cov_cutoff | n/a | coverage cutoff value (a positive float number ) | float? |
iontorrent | n/a | true if Libraries are IonTorrent reads. | boolean |
sc | n/a | This option is required for MDA. true if single-cell data. | boolean |
onlyassembler | n/a | Run only assembly if true (without read error correction) | boolean |
careful | n/a | Careful correction. Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector, a post processing tool, which uses BWA tool (comes with SPAdes). | boolean |
Steps
ID | Name | Description |
---|---|---|
unicycler | ||
spades | ||
bandage_image_unicycler | ||
bandage_info_unicycler | ||
bandage_image_spades | ||
bandage_info_spades |
Outputs
ID | Name | Description | Type |
---|---|---|---|
out_contigs_spades | n/a | n/a | File |
out_scaffolds_spades | n/a | n/a | File |
out_contig_stats_spades | n/a | n/a | File |
out_scaffold_stats_spades | n/a | n/a | File |
assembly_graph_spades | n/a | n/a | File |
assembly_graph_with_scaffolds_spades | n/a | n/a | File |
all_log_spades | n/a | n/a | File[] |
assembly_image_spades | n/a | n/a | File |
assembly_info_spades | n/a | n/a | File |
assembly_graph_unicycler | n/a | n/a | File |
assembly_unicycler | n/a | n/a | File |
assembly_image_unicycler | n/a | n/a | File |
assembly_info_unicycler | n/a | n/a | File |

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Views: 760 Downloads: 37
Created: 10th Apr 2020 at 11:45
Last updated: 30th Jun 2020 at 09:05
Last used: 19th Jan 2021 at 13:14

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