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perf: Ont downsampling normalization #489

Merged
merged 62 commits into from
Mar 15, 2022
Merged

perf: Ont downsampling normalization #489

merged 62 commits into from
Mar 15, 2022

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simakro
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@simakro simakro commented Feb 28, 2022 •
edited by alethomas
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Description

downsampling and clipping of ONT reads handled by notramp

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simakro and others added 13 commits February 15, 2022 10:02
@simakro
wrote new script map_bin_amp_sampler.py for 'normalizing' reducing/co…
a951fcb 
…verage on each amplicon to a common cutoff and started modifying rule long_read.smk to do the reuired mapping and run the script
@simakro
added write out and convert of picked reads from source fastq to out-…
b9bafe8 
…fasta
@simakro
change in- and output file-extensions for all rules downstream of cap…
420e3a7 
…_cov_amp from fastq to fasta; changed also in get_reads_by_stage
@simakro
fixed several snakemake related bugs
d853977
@simakro
multiple restorations to repair broken workflow
c303aa8
@simakro
established custom script for trimming of primers work-title: map-trim
e77580c
@simakro
improved coverage-capping amp_covcap_sampler.py and amplicon primer-t…
35ca8ad 
…rimming map_trim.py scripts, including reverse strand swap for trimming
@simakro
added improved logic for clipping of '-' strand aligning reads
6412c6f
@simakro
use only one map-trim to remove all, reinstated porechop; multiple ad…
85f5a58 
…aptations and fixes in assembly.smk, common.smk, long_read.smk, qc.smk, amp_covcap_sampler.py, map_trim.py; repaired workflow and changed naming patterns and formatting for ont; medaka rule -v; get_reads_by_stage, get trimmed reads, species diversity_before_se, seqtk.yaml
@simakro
remove map-trim in order to reorganize
4372ab6
@simakro
perform all clipping and downsampling with notramp
b62d62e
@simakro
multiple renamings and adaptions
931f4d6
@simakro
cleanup
e17b32f
@simakro simakro changed the title perf:Ont downsampling normalization perf: Ont downsampling normalization Feb 28, 2022
alethomas
alethomas previously requested changes Mar 1, 2022
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thomasbtf
thomasbtf previously requested changes Mar 2, 2022
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@simakro simakro dismissed stale reviews from thomasbtf and alethomas March 12, 2022 10:47

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simakro
simakro commented Mar 14, 2022
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Was soll hier geändert worden sein? Ich denke auch nicht, das es einen 25-45 Primer gibt.

@thomasbtf
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thomasbtf commented Mar 14, 2022 •
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There is a new snakemake release: https://github.com/snakemake/snakemake/releases/tag/v7.2.1

Let's hope that fixes the report problem.

simakro
simakro commented Mar 15, 2022
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Hard coded path geht natürlich gar nicht.

thomasbtf
thomasbtf approved these changes Mar 15, 2022
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LGTM!

@thomasbtf thomasbtf merged commit f502dd2 into master Mar 15, 2022
@thomasbtf thomasbtf deleted the ont_downsampling_normalization branch March 15, 2022 17:38
@github-actions github-actions bot mentioned this pull request Mar 15, 2022
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@thomasbtf thomasbtf thomasbtf approved these changes

@alethomas alethomas Awaiting requested review from alethomas

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3 participants
@simakro @thomasbtf @alethomas