GTN Training - Antibiotic Resistance Detection
Version 1

Workflow Type: Galaxy
Stable

Workflow for the GTN training "Antibiotic resistance detection"

Steps

ID Name Description
0 Plasmids
1 NanoPlot toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1
10 NanoPlot toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1
11 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17
12 Racon toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1
2 Map with minimap2 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17
3 Create assemblies with Unicycler toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0
4 miniasm toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0
5 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0
6 PlasFlow toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0
7 staramr toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1
8 Bandage Image toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0
9 GFA to FASTA toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0

Outputs

ID Name Description Type
output_html output_html n/a
nanostats nanostats n/a
nanostats_post_filtering nanostats_post_filtering n/a
read_length read_length n/a
log_read_length log_read_length n/a
output_html output_html n/a
nanostats nanostats n/a
nanostats_post_filtering nanostats_post_filtering n/a
read_length read_length n/a
log_read_length log_read_length n/a
alignment_output alignment_output n/a
consensus consensus n/a
alignment_output alignment_output n/a
assembly_graph assembly_graph n/a
assembly assembly n/a
gfa gfa n/a
outfile outfile n/a
probability_table probability_table n/a
chromosomes chromosomes n/a
plasmids plasmids n/a
unclassified unclassified n/a
blast_hits blast_hits n/a
summary summary n/a
detailed_summary detailed_summary n/a
resfinder resfinder n/a
plasmidfinder plasmidfinder n/a
settings settings n/a
excel excel n/a
outfile outfile n/a
out_fa out_fa n/a

Version History

Version 1 (earliest) Created 24th Nov 2022 at 13:28 by Saskia Hiltemann

Initial commit


Open master d5cadd9
help Creators and Submitter
Activity

Views: 78

Created: 24th Nov 2022 at 13:28

Last used: 8th Dec 2022 at 08:51

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Total size: 24.8 KB
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