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Try to fix RRA #214

Merged
merged 12 commits into from
Nov 8, 2024
Merged

Try to fix RRA #214

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886228c
Try to fix RRA
LaurenceKuhl Oct 29, 2024
b345455
Merge branch 'dev' into dev
LaurenceKuhl Oct 29, 2024
45eb416
Add singularity to the CI
LaurenceKuhl Oct 29, 2024
a0b30ee
Merge branch 'dev' of github.com:laurencekuhl/crisprseq into dev
LaurenceKuhl Oct 29, 2024
1ea9a93
Add temp location
LaurenceKuhl Oct 29, 2024
c6f5c19
try defining BIOMART_CACHE for mageck flute
mirpedrol Oct 29, 2024
9f0de4f
Modified to fix template_fluteMLE.R for Apptainer/Singularity
medmaca Nov 1, 2024
84a919a
Modified graphrra.nf for Apptainer/Singularity.
medmaca Nov 7, 2024
39f5f54
pre commit
LaurenceKuhl Nov 8, 2024
a7bc829
Update changelog
LaurenceKuhl Nov 8, 2024
5316dc9
Add Matthew as a conntributer
LaurenceKuhl Nov 8, 2024
957b5f2
Update .github/workflows/ci.yml
LaurenceKuhl Nov 8, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -41,7 +41,7 @@ jobs:
- "test_umis"
- "test_screening_count_table"
isMaster:
- ${{ github.base_ref == 'master' }}
- true
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Are you sure you want this to always run? That seems sort of overkill in terms of the polarbears (this would be every single CI run you will run 3 profiles x 6 tests x 2 nextflow version everytime...?

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no you're right i think we wanted to just run it for this PR, let me modify it

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I would suggest to test singularity manually by opening a draft PR against master (just don't merge it)

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# Exclude conda and singularity on dev
exclude:
- isMaster: false
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fix design matrix bug that introduced dots instead of a hyphen ([#190](https://github.com/nf-core/crisprseq/pull/190))
- Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty ([#190](https://github.com/nf-core/crisprseq/pull/190))
- Fix a typo in crisprcleanr/normalize, when a user inputs a file ([#192](https://github.com/nf-core/crisprseq/pull/192))
- Add Singularity and Docker tests in the CI, also fix any issues users had when running MAGeCKFlute with Docker or Singularity. ([#214](https://github.com/nf-core/crisprseq/pull/214))

### General

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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -136,6 +136,7 @@ We thank the following people for their extensive assistance in the development
- [@jianhong](https://github.com/jianhong)
- [@joannakraw](https://github.com/joannakraw)
- [@mashehu](https://github.com/mashehu)
- [@medmaca](https://github.com/medmaca)
- [@metinyazar](https://github.com/metinyazar)
- [@msanvicente](https://github.com/msanvicente)
- [@mschaffer-incyte](https://github.com/mschaffer-incyte)
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5 changes: 1 addition & 4 deletions modules/local/mageck/graphrra.nf
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Expand Up @@ -27,11 +27,10 @@ process MAGECK_GRAPHRRA {
#### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text.
####
#### Orient a reference sequence according to reads orientation.

Sys.setenv(HOME = getwd()) # Required for Singularity/Apptainer
library(MAGeCKFlute)
library(ggplot2)
options(ggrepel.max.overlaps = Inf)

gdata = ReadRRA("$gene_summary")
gdata <- transform(gdata, LogFDR = -log10(FDR))
png(filename = paste0("$meta.treatment","_vs_","$meta.reference","_scatterview.png"), width = 6, height = 4, units = "in", res = 300)
Expand Down Expand Up @@ -60,6 +59,4 @@ process MAGECK_GRAPHRRA {
writeLines(version_ggplot, f)
close(f)
"""


}
9 changes: 2 additions & 7 deletions templates/template_fluteMLE.R
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Expand Up @@ -4,13 +4,8 @@
####
#### graphs mageck MLE

# Required to fix corrupted cache from Singularity container
library(BiocFileCache)
bfc <- BiocFileCache("~/.cache/R/ExperimentHub")
res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE)
bfcremove(bfc, rids=res\$rid)
library(ExperimentHub)
eh = ExperimentHub()
# Required to fix .cache issue with Singularity/Apptainer container
Sys.setenv(HOME = getwd())

library(MAGeCKFlute)
library(clusterProfiler)
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