Metavisitor: Workflow for Use Case 3-3
Created: 2016-05-13 08:45:32
Last updated: 2016-05-13 08:46:55
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Workflow Components
Inputs (2)
| Name |
Description |
| Patient sequence collection |
|
| Nucleotide Viral Blast Database |
|
Steps (13)
| Name |
Tool |
Description |
| Input dataset collection |
None |
|
| Input dataset |
None |
|
| NCBI BLAST+ blastn |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07 |
|
| blast_to_scaffold |
toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0 |
|
| Concatenate multiple datasets |
toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2 |
|
| Retrieve FASTA from NCBI |
toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4 |
|
| Bowtie2 |
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2 |
|
| NCBI BLAST+ makeblastdb |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.07 |
|
| Trinity |
toolshed.g2.bx.psu.edu/repos/anmoljh/trinityrnaseq/trinityrnaseq/r20140717 |
|
| Regex Find And Replace |
toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0 |
|
| NCBI BLAST+ blastn |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07 |
|
| Parse blast output and compile hits |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3 |
|
| Concatenate multiple datasets |
toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2 |
|
Outputs (22)
| Name |
Type |
| output1 |
tabular |
| output |
fasta |
| out_file1 |
input |
| outfilename |
fasta |
| logfile |
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 |
| outfile |
data |
| trinity_log |
txt |
| assembled_transcripts |
fasta |
| out_file1 |
input |
| output1 |
tabular |
| tabularOutput |
tabular |
| fastaOutput |
fasta |
| al_sequences |
fasta |
| un_sequences |
fasta |
| out_file1 |
input |
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