Cloud dev - #89

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snalty wants to merge 32 commits into

cloudfrom

Commits on Dec 5, 2025

nextflow and containers
snalty
committed
2642b8c

Commits on Dec 12, 2025

working demux
snalty
committed
6ac4fc3

Commits on Dec 18, 2025

rework demultiplex for correct file output
snalty
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7094a46
Add comments for channel generation
snalty
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58899fe
Update container files
snalty
committed
45196f0
break out rna fastq channel to variable
snalty
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329d150
Add app process
snalty
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b7db42e
Add analysis subworkflow
snalty
committed
ae84d07
Add beginning of QC workflow
snalty
committed
fc45887
add sample qc file creation
snalty
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05d4ff2
add merging qc files
snalty
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20bfbf4
import subworkflows
snalty
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98c4756
add database generation workflow
snalty
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eb42b9f
add sample sheet filtering workflow
snalty
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8ce1b26
move scripts to bin dir and add uv shebang
snalty
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00c84b4
Remove legacy scripts
snalty
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22c8c8e
Remove legacy sub scripts
snalty
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3792725
Remove unused read count visualisation
snalty
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507d04c
Remove conda envs
snalty
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ec4c7cc

Commits on Dec 22, 2025

reinclude contamination script
snalty
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09ee3e8
remove contamination from scripts dir
snalty
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b215a2b
Include missing outputs and scripts
snalty
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f07eec5
remove debug view from channel
snalty
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5be9417
publish contamination file
snalty
committed
63e588b

Commits on May 20, 2026

Add gh action to make container
erikwaskiewicz
committed
4023d85
edit gh action
erikwaskiewicz
committed
69f2e98
Undo change to gh action (was only to get it to register as an action within github)
erikwaskiewicz
committed
acc32f1
add paths to containerfile
erikwaskiewicz
committed
5e03461
First attempt at running in landing zone
erikwaskiewicz
committed
ee87528
Edit samplesheet script to handle LIMS samplesheets
erikwaskiewicz
committed
bf58fe0

Commits on May 21, 2026