naobservatory mgs-pipeline issues

naobservatory / mgs-pipeline

MIT License

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issues

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Update the taxonomy and reference DBs

#65 jeffkaufman closed 3 weeks ago
1
Added Leung 2021 (Metasub study of air in metro systems across the globe)

#64 simonleandergrimm closed 4 months ago
0
Simon rosario 2018

#63 simonleandergrimm closed 5 months ago
0
Ran Prussin 2019 through mgs-pipeline.

#62 simonleandergrimm closed 5 months ago
0
Fixing a small bug in ribo_frac.

#61 simonleandergrimm closed 5 months ago
3
dashboard: update instructions for pushing data live

#60 jeffkaufman closed 5 months ago
0
Simon add belstrom 2017

#59 simonleandergrimm closed 5 months ago
3
Riboreads fails on bioproject PRJNA396840, sample SRR5892185

#58 simonleandergrimm closed 1 month ago
1
ribofrac: fix typo

#57 jeffkaufman closed 6 months ago
1
Fix import-accession and metadata for Grumaz 2016

#56 lennijusten closed 6 months ago
1
classifier-comparison: first cut at classifier framework

#55 jeffkaufman closed 6 months ago
0
Pipeline: Allow parallelizing at the sample level

#54 jeffkaufman closed 6 months ago
2
running prepare-dashboard.sh on main without other edits.

#53 simonleandergrimm closed 6 months ago
6
Reformatted all .py scripts with black. Deleted bioprojects/PRJNA774620/metadata/prepare-metadata.py

#52 simonleandergrimm closed 7 months ago
1
Added check.sh to the repository. Checks if all Python scripts are formatted with black.

#51 simonleandergrimm closed 7 months ago
0
alignments: additionally align against human genome

#50 jeffkaufman closed 7 months ago
0
Added locations to Bohl 2022 (Cambodia) and Wu 2020 (Wuhan). Reran prepare_dashboard.sh

#49 simonleandergrimm closed 6 months ago
6
Add plasma papers

#48 lennijusten closed 6 months ago
1
alignments: align all reads, not just hvreads

#47 jeffkaufman closed 7 months ago
3
Bowtie: mask low-complexity sequences

#46 jeffkaufman closed 7 months ago
0
Automatically add sample metadata when importing new bioprojects

#45 lennijusten closed 7 months ago
2
build bowtie: avoid duplicates

#44 jeffkaufman closed 7 months ago
0
bowtie: minor fixes after running bowtie across all existing data

#43 jeffkaufman closed 7 months ago
0
dashboard: more reworking

#42 jeffkaufman closed 7 months ago
0
dashboard: stop using data.js, and pull individual json files instead

#41 jeffkaufman closed 7 months ago
0
dashboard: start breaking out per-bioproject counts

#40 jeffkaufman closed 7 months ago
0
Dashboard: check in first half of Tisza 2023 data

#39 jeffkaufman closed 7 months ago
1
Alignments: add a new pipeline stage that runs Bowtie2

#38 jeffkaufman closed 7 months ago
0
bowtie: make map for interpreting genome ids

#37 jeffkaufman closed 7 months ago
2
Add a script for reprocessing all the bioprojects in parallel

#36 jeffkaufman closed 7 months ago
2
Simon bowtie2 db

#35 simonleandergrimm closed 7 months ago
3
dashboard: fix bug where we were getting zero counts for human-infecting viruses

#34 jeffkaufman closed 7 months ago
0
Add ribofrac data to dashboard

#33 lennijusten closed 8 months ago
3
implement readlengths

#32 jeffkaufman closed 7 months ago
2
Add new stage, samplereads

#31 jeffkaufman closed 8 months ago
0
Ribofrac: Check for empty files and skip samples with zero reads

#30 lennijusten closed 8 months ago
3
Added kraken assignment to creation of hvreads.

#29 simonleandergrimm closed 8 months ago
1
Save "nan" for ribofrac when sample has zero reads

#28 lennijusten closed 8 months ago
0
dashboard: add ribofrac data

#27 lennijusten closed 8 months ago
1
ribofrac: add dashboard files

#26 lennijusten closed 8 months ago
1
Get rRNA fraction with fast ribocounts()

#25 lennijusten closed 8 months ago
0
Adding feature to ribocounts that saves non-rRNA read IDs

#24 lennijusten closed 8 months ago
1
Run Langenfeld data

#23 dp-rice closed 9 months ago
4
Add ribocounts dashboard data

#22 lennijusten closed 9 months ago
2
Add ribcounts to sample metadata for dashboard deployment

#21 lennijusten closed 9 months ago
0
Add Lagenfeld 2022

#20 dp-rice closed 9 months ago
1
Adding Riquelme 2022 to dashboard, attempt 2

#19 willbradshaw closed 9 months ago
3
Read counting isn't correct

#18 jeffkaufman closed 9 months ago
1
Prepared metadata for Riquelme 2022

#17 willbradshaw closed 9 months ago
0
Adding RiboDetector to MGS pipeline

#16 lennijusten closed 9 months ago
2