AMR detection workflow - CFIA
Version 1

Workflow Type: Galaxy
No description specified

Inputs

ID Name Description Type
input_type_cond input_type_cond runtime parameter for tool BBTools: BBduk n/a
library library runtime parameter for tool Shovill n/a
library library runtime parameter for tool Shovill n/a
library library runtime parameter for tool Shovill n/a
library library runtime parameter for tool Shovill n/a
input_type input_type runtime parameter for tool Map with BWA n/a
reference_source reference_source runtime parameter for tool Map with BWA n/a
input_type input_type runtime parameter for tool Map with BWA n/a
reference_source reference_source runtime parameter for tool Map with BWA n/a
auto_selection auto_selection runtime parameter for tool pilon n/a
reference_genome reference_genome runtime parameter for tool pilon n/a
auto_selection auto_selection runtime parameter for tool pilon n/a
reference_genome reference_genome runtime parameter for tool pilon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
input input runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
adv_param adv_param runtime parameter for tool MOB-Recon n/a
input input runtime parameter for tool MOB-Recon n/a
input_fastas input_fastas runtime parameter for tool sistr_cmd n/a
report report runtime parameter for tool hamronize n/a
reports reports runtime parameter for tool hamronize: summarize n/a

Steps

ID Name Description
0 Input dataset collection
1 BBTools: BBduk toolshed.g2.bx.psu.edu/repos/iuc/bbtools_bbduk/bbtools_bbduk/1.0.0+galaxy3
2 Shovill toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
3 Shovill toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1
4 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
5 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
6 pilon toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1
7 pilon toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1
8 MOB-Recon toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/3.0.3+galaxy0
9 MOB-Recon toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/3.0.3+galaxy0
10 sistr_cmd toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1+galaxy1
11 hamronize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1
12 hamronize: summarize toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2

Outputs

ID Name Description Type
outputu outputu n/a
outputu2 outputu2 n/a
outputm outputm n/a
outputm2 outputm2 n/a
outputs outputs n/a
shovill_std_log shovill_std_log n/a
contigs contigs n/a
contigs_graph contigs_graph n/a
shovill_std_log shovill_std_log n/a
contigs contigs n/a
contigs_graph contigs_graph n/a
bam_output bam_output n/a
bam_output bam_output n/a
output_fasta output_fasta n/a
output_fasta output_fasta n/a
plasmids plasmids n/a
contig_report contig_report n/a
mobtyper_aggregate_report mobtyper_aggregate_report n/a
chromosome chromosome n/a
plasmids plasmids n/a
contig_report contig_report n/a
mobtyper_aggregate_report mobtyper_aggregate_report n/a
chromosome chromosome n/a
output_prediction_tab output_prediction_tab n/a
cgmlst_profiles cgmlst_profiles n/a
novel_alleles novel_alleles n/a
alleles_output alleles_output n/a
output_tsv output_tsv n/a
output_tsv output_tsv n/a

Version History

Version 1 (earliest) Created 24th Nov 2022 at 13:42 by Dennis Dollée

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Open master 0958f3b
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Created: 24th Nov 2022 at 13:42

Last used: 6th Dec 2022 at 19:09

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