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Integrate spike handling to main #64

Merged
merged 34 commits into from
Jun 6, 2024
Merged

Integrate spike handling to main #64

merged 34 commits into from
Jun 6, 2024

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rmcolq
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@rmcolq rmcolq commented May 15, 2024

Add support for spike ins:

  • checks for spike ins and adds boolean to kraken summary json
  • creates separate QC output files summarizing if specified spikes were found either by mapping or classification, and the counts/percentages
  • slight reorganization of repeated code

@rmcolq
rebasing
46a44e2
@rmcolq
update outputing of json
76cecdf
@rmcolq
reapply fixes
997739e
@rmcolq
remove zymo communities from spike in list
ca637f9
@rmcolq
convert warning file to json
7b62588
@rmcolq
WIP: updates to test on server
9a304c9
@rmcolq
WIP: updates to test on server
d0ec569
@rmcolq
save for future reference - filtering spike ins with mapping
25e101f
@rmcolq
refactor spike in handling to NOT filter them, but to provide a usefu…
7b427e4 
…l summary of whether the input spike ins were found and counts
@rmcolq
handle illumina
75e1ca8
@rmcolq
Merge pull request #63 from rmcolq/hcid_to_json
ad8d4d4 
convert warning file to json
@rmcolq
update test
e2d19a5
@rmcolq
add mapped_percentage
3a0acae
@rmcolq
Merge pull request #62 from rmcolq/remove_spike_ins
f6ac80f 
Remove spike ins
@rmcolq
specify that resource dir is in projectDir
3c9f530
@rmcolq
ERCC_92->ERCC-RNA_4456740
3221e71
@rmcolq
add MS2 phage
7d03a5b
@rmcolq
explicitly cast taxa as strings
7ec4e0c
@rmcolq
fix typo
573ff7c
@rmcolq
fix spike refs
400c8af
@rmcolq
add pycache to gitignore
570bece
@rmcolq
add .ipynb_checkpoints to gitignore
38d4835
@rmcolq
add a line to report acknowledging ONT sankey
fc1690c
@rmcolq
add taxid and taxon human readable name to the spike refs, and pass t…
be8183c 
…he info through to spike_count_summary.json
@rmcolq
remove repeat segment_name
a252e7d
@rmcolq
Merge pull request #65 from rmcolq/add_to_spike_info
235c6bc 
add taxid and taxon human readable name to the spike refs, and pass t…
@rmcolq
add an error code if spike in not interpretable, add 0 values to outp…
0194a59 
…ut summary if no mapped/classified reads found
@rmcolq
update spike output name matching
8b9a604
@rmcolq
proportion not percentage
9043b2e
@rmcolq
bugfix
4fb3583
@rmcolq rmcolq merged commit dff1d41 into main Jun 6, 2024
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