Merge pull request #214 from LaurenceKuhl/dev

Fix MAGeCKFlute issues

CHANGELOG.md

@@ -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
 

README.md

@@ -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)

modules/local/mageck/graphrra.nf

@@ -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)
@@ -60,6 +59,4 @@ process MAGECK_GRAPHRRA {
     writeLines(version_ggplot, f)
     close(f)
     """
-
-
 }

templates/template_fluteMLE.R

@@ -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)