Docker r-bolero 1.2 docker profile functionning

src/.docker_modules/r-bolero/1.2/Dockerfile

@@ -18,12 +18,11 @@ RUN apt-get update \
 		libjpeg-dev \
 		procps
 
-## copy Rscript files
-COPY ./*.R .
+## Copy Rscript files
+COPY ./*.R /
 
 ## Install packages
 RUN Rscript Install_packages.R
 
 ## Langage
-CMD ["bash"]
-
+CMD ["bash"]
\ No newline at end of file

src/.docker_modules/r-bolero/1.2/HBV_RNAs_count.R

@@ -13,7 +13,7 @@ conflict_prefer("filter", "dplyr")
 conflict_prefer("lag", "dplyr")
 
 # source graphical theme:
-source(file="ggplot_theme_publication-2.R")
+source(file="/ggplot_theme_publication-2.R")
 
 # Load files
 option_list = list(

src/.docker_modules/r-bolero/1.2/Install_packages.R

-list.of.packages <- c("ggplot2", "tidyr", "dplyr", "tidyverse", "stringr", "optparse", "RColorBrewer", "conflicted", "BiocManager", "resshape2", "R.utils", "conflicted", "future", "future.apply")
+list.of.packages <- c("devtools", "tidyverse", "ggplot2", "ggthemes", "tidyr", "dplyr", "stringr", "optparse", "RColorBrewer", 
+                      "conflicted", "BiocManager", "resshape2", "R.utils", "conflicted", "future", "future.apply")
 new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
-if(length(new.packages)) install.packages(new.packages, dependencies = T)
+if(length(new.packages)) install.packages(new.packages, dependencies = T) # , lib = "/usr/local/lib/R/library"
\ No newline at end of file

src/.docker_modules/r-bolero/1.2/Start_positions.R

@@ -14,7 +14,7 @@ conflict_prefer("filter", "dplyr")
 conflict_prefer("lag", "dplyr")
 
 # source graphical theme:
-source(file="ggplot_theme_publication-2.R")
+source(file="/ggplot_theme_publication-2.R")
 
 # Load Start_positions_count files:
 option_list = list(

src/.docker_modules/r-bolero/1.2/docker_init.sh

-docker build src/.docker_modules/r-bolero/1.1 -t 'xgrand/r-bolero:1.1'
-docker push xgrand/r-bolero:1.1
+docker build src/.docker_modules/r-bolero/1.2 -t 'xgrand/r-bolero:1.2'
+docker push xgrand/r-bolero:1.2

src/nf_modules/porechop/main.nf

@@ -3,6 +3,7 @@ container_url = "xgrand/porechop:${version}"
 
 params.porechop_out = ""
 process porechop {
+    errorStrategy 'ignore'
     container = "${container_url}"
     label "big_mem_multi_cpus"
     tag "$barcode"

src/nf_modules/rna_count/main.nf

-version = "1.1"
+version = "1.2"
 container_url = "xgrand/r-bolero:${version}"
 
 params.rna_count_out = ""

src/nf_modules/start_positions/main.nf

-version = "1.1"
+version = "1.2"
 container_url = "xgrand/r-bolero:${version}"
 
 params.start_position_counts_out =""