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Incorporate vibrio characterisation with srst2 into TheiaProk workflows #216

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merged 31 commits into from
Apr 13, 2023
Merged

Incorporate vibrio characterisation with srst2 into TheiaProk workflows #216

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7c12fee
add working version with local docker image - To be updated
cimendes Feb 24, 2023
40ae0db
parse output tsv
cimendes Feb 27, 2023
904ba4e
remove comment
cimendes Feb 27, 2023
8b93c5f
improvements to tsv parsing
cimendes Feb 27, 2023
c629fa5
update docker
cimendes Feb 27, 2023
eb77bf9
update gene_db path
cimendes Feb 27, 2023
e6ae8a2
allow for single end reads
cimendes Feb 27, 2023
4cbb1ee
add vibrio to merlin magic
cimendes Feb 27, 2023
ed44e6e
add vibrio typing to theiaprok_illumina_pe and theiaprok_illumina_se…
cimendes Feb 27, 2023
74fadcf
unsatisfactory solution to read name issue with clean reads on srst2 …
cimendes Feb 27, 2023
8980632
update md5sum for gambit
cimendes Feb 28, 2023
bebfaa8
Merge branch 'main' into im-vibrio-srst2
cimendes Feb 28, 2023
9d9b75d
Bringing in recent changes from main into this im-vibrio-srs2 branch.…
kapsakcj Mar 16, 2023
1ffd357
added srst2 outputs to input call block for export_taxon_tables in bo…
kapsakcj Mar 17, 2023
e07446d
fixed syntax in export_taxon_tables python dictionary
kapsakcj Mar 17, 2023
9b762a6
add additional output file: detailed TSV output from SRST2. Also adde…
kapsakcj Mar 17, 2023
5cea6c5
added new output file srst2_vibrio_detailed_tsv to PE, SE, and merlin…
kapsakcj Mar 17, 2023
8b33b5a
update parsing block to account for when output columns do not exist
cimendes Mar 20, 2023
c1a0b7b
remove duplicated block
cimendes Mar 20, 2023
99d01e0
expose srst2 parameters in merlin_magic
cimendes Mar 20, 2023
6db886c
fix CI with updated checksum
cimendes Mar 20, 2023
13abff2
add function to translate srst2 mismatch/uncertanty indicators to hum…
cimendes Mar 27, 2023
0e29cea
replace not found hits with "(not detected)" so it's more human readable
cimendes Mar 28, 2023
33d5f66
altered srst2_vibrio parsing: ctxA, ompW and toxR are being reported …
cimendes Mar 29, 2023
4e4116a
deprecate srst2_results_tsv file from output; remove trailing empty s…
cimendes Mar 29, 2023
ccad72a
fix merlin magic export mistake
cimendes Mar 29, 2023
c6cc642
fix more oops mistakes
cimendes Mar 29, 2023
3029eea
update srsrt2_vibrio default paramenters to be less stringent
cimendes Mar 31, 2023
32068c3
rename output column from srst2_vibrio_serotype to srst2_vibrio_serog…
cimendes Apr 5, 2023
4c1e70c
update container for staphb/srst2:0.2.0-vcholerae
cimendes Apr 6, 2023
a7ad2ff
Update task_srst2_vibrio.wdl
kevinlibuit Apr 13, 2023
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6 changes: 3 additions & 3 deletions workflows/wf_merlin_magic.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -47,11 +47,11 @@ workflow merlin_magic {
Boolean call_shigeifinder_reads_input = false
Boolean tbprofiler_additional_outputs = false
String output_seq_method_type = "WGS"
Int srst2_min_cov = 90
Int srst2_max_divergence = 10
Int srst2_min_cov = 80
Int srst2_max_divergence = 20
Int srst2_min_depth = 5
Int srst2_min_edge_depth = 2
Int srst2_gene_max_mismatch = 10
Int srst2_gene_max_mismatch = 200
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Maybe it should be increased further

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@emmadoughty

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Resloved?

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Seems that the validation runs linked above don't have these values set by merlin magic--which leads me to assume that they're just using default srst2 values (i.e. 10).

}
if (merlin_tag == "Acinetobacter baumannii") {
call kaptive.kaptive {
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