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feat: Merge trimming and mapping update; resolves #8, resolves #9, resolves #10 #19

Merged
merged 23 commits into from
Feb 24, 2022
Merged

feat: Merge trimming and mapping update; resolves #8, resolves #9, resolves #10 #19

merged 23 commits into from
Feb 24, 2022

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sroener
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@sroener sroener commented Feb 24, 2022

Changes

additions

  • option to use trimmomatic for read processing

  • add rule for downloading default illumna adapter sequences

  • add rule for trimming PE reads

  • add rule for trimming SE reads

  • add option for using only paired end data (don't use singletons)

refactor

  • move trimming to separate snakefile
  • move filtering to separate snakefile

update

  • update bwa to bwa-mem2 for mapping
  • add wrapper to handle mapping in a more flexible way

sroener added 23 commits February 17, 2022 11:55
@sroener
add rule to download illumina adapter from trimmomatic repo
af854c3
@sroener
change name of get_NGmerge_input to get_trimming_input
320497b
@sroener
move NGmerge to trimming rule; add trimmomatic to trimming rule
8629006
@sroener
add separate trimming rule
d026f91
@sroener
parse trimmomatic options from config.yaml; return properly formatted…
3d93a4f 
… trimming options
@sroener
add trimmomatic SE rule
153574e
@sroener
add option to configure min read length for filtering
2f4a8f3
@sroener
move length filter for NGmerge to filtering.smk
2452ac9
@sroener
remove common.py
7cf472e
@sroener
add README.md, containing info on NGmerge
7b3d1d1
@sroener
initial commit
344fc92
@sroener
add notes on bwa-mem2
60e73c9
@sroener
substitute bwa with bwa-mem2
c54d8d7
@sroener
add separate filtering rule
54a790e
@sroener
substitute bwa indexing with bwa-mem2 version
a21ccc7
@sroener
initial commit
0e4a574
@sroener
update mapping from bwa to bwa-mem2
4b4be9b
@sroener
update notes section
92f4419
@sroener
add new options for trimming and mapping
c9fa7f8
@sroener
remove intermediate files aufter processing
e212d06
@sroener
add input function for mapping
4f99fdf
@sroener
refactor: reorder of rules
62c827f
@sroener
Merge branch 'bwa-mem2_integration' into develop
bd7f24d
@sroener sroener merged commit 6d91d65 into main Feb 24, 2022
@sroener sroener linked an issue Feb 24, 2022 that may be closed by this pull request
Add option to use merged reads only #10
Closed
@sroener sroener changed the title feat: Merge trimming and mapping update; resolves #8, resolves #9 #10 feat: Merge trimming and mapping update; resolves #8, resolves #9, resolves #10 Feb 24, 2022
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Add option to use merged reads only
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@sroener