Metavisitor: Workflow for Use Case 3-2
Created: 2016-05-13 08:42:03
Last updated: 2017-04-17 15:54:26
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Workflow Components
Inputs (2)
| Name |
Description |
| Patient sequences collection |
|
| Nucleotide Viral BLAST database |
|
Steps (11)
| Name |
Tool |
Description |
| Input dataset collection |
None |
|
| Input dataset |
None |
|
| Concatenate multiple datasets |
toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2 |
|
| Bowtie2 |
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2 |
|
| Bowtie2 |
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2 |
|
| Group |
Grouping1 |
|
| FASTQ to FASTA |
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0 |
|
| Sort |
sort1 |
|
| Oases_optimiser |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.2.1 |
|
| NCBI BLAST+ blastn |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08 |
|
| Parse blast output and compile hits |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3 |
|
Outputs (24)
| Name |
Type |
| out_file1 |
input |
| output_unaligned_reads_l |
fastqsanger |
| output_aligned_reads_l |
fastqsanger |
| output_aligned_reads_r |
fastqsanger |
| output_unaligned_reads_r |
fastqsanger |
| output |
bam |
| output_sam |
sam |
| mapping_stats |
txt |
| output_unaligned_reads_l |
fastqsanger |
| output_aligned_reads_l |
fastqsanger |
| output_aligned_reads_r |
fastqsanger |
| output_unaligned_reads_r |
fastqsanger |
| output |
bam |
| output_sam |
sam |
| mapping_stats |
txt |
| out_file1 |
tabular |
| output |
fasta |
| out_file1 |
input |
| transcripts |
fasta |
| output1 |
tabular |
| tabularOutput |
tabular |
| fastaOutput |
fasta |
| al_sequences |
fasta |
| un_sequences |
fasta |
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Version 2 (latest)
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