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Fix custom anchors for kraken #2170

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merged 5 commits into from
Nov 13, 2023
Merged

Fix custom anchors for kraken #2170

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1f8f528
fix custom anchors for kraken
jchorl Nov 10, 2023
260801e
[automated] Update CHANGELOG.md
multiqc-bot Nov 10, 2023
dc786ff
Pass sp_key from bracken to kraken
vladsavelyev Nov 13, 2023
a614c05
Merge branch 'master' into jchorl/krakenanchors
vladsavelyev Nov 13, 2023
8971052
Changelog
vladsavelyev Nov 13, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
- Nanostat: account for both tab and spaces in v1.41+ search pattern ([#2155](https://github.com/ewels/MultiQC/pull/2155))
- Clean version strings with build IDs ([#2166](https://github.com/ewels/MultiQC/pull/2166))
- Remove position:absolute from table values ([#2169](https://github.com/ewels/MultiQC/pull/2169))
- Fix custom anchors for kraken ([#2170](https://github.com/ewels/MultiQC/pull/2170))

### New Modules

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1 change: 1 addition & 0 deletions multiqc/modules/bracken/bracken.py
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Expand Up @@ -21,4 +21,5 @@ def __init__(self):
href="https://ccb.jhu.edu/software/bracken/",
info="is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.",
doi="10.7717/peerj-cs.104",
sp_key="bracken",
)
3 changes: 2 additions & 1 deletion multiqc/modules/kraken/kraken.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ def __init__(
href="https://ccb.jhu.edu/software/kraken/",
info="is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.",
doi="10.1186/gb-2014-15-3-r46",
sp_key="kraken",
):
super(MultiqcModule, self).__init__(
name=name,
Expand All @@ -48,7 +49,7 @@ def __init__(
# Find and load any kraken reports
self.kraken_raw_data = dict()
new_report_present = False
for f in self.find_log_files(self.anchor, filehandles=True):
for f in self.find_log_files(sp_key, filehandles=True):
log_version = self.get_log_version(f)
f["f"].seek(0)
if log_version == "old":
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