Merge pull request #71 from EPPIcenter/changes-for-v0.0.9

Changes for v0.0.9

Apptainer

@@ -3,7 +3,7 @@ From: rocker/r-ubuntu:22.04
 
 %post
 
-apt-get update && apt-get install -y build-essential python3-pip libbz2-dev libsdl1.2-dev liblzma-dev libcurl4-openssl-dev zlib1g-dev libxml2-dev libssl-dev r-cran-tidyverse trf bwa bcftools samtools default-jre && rm -rf /var/lib/apt/lists/*
+apt-get update && apt-get install -y build-essential python3-pip libbz2-dev libsdl1.2-dev liblzma-dev libcurl4-openssl-dev zlib1g-dev libxml2-dev libssl-dev trf bwa bcftools samtools default-jre pandoc && rm -rf /var/lib/apt/lists/*
 pip install cutadapt==4.1
 
 mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
@@ -12,6 +12,7 @@ R -e 'install.packages("remotes")'
 
 # Update apt-get
 Rscript -e 'install.packages("remotes", version = "2.4.2")'
+Rscript -e 'remotes::install_cran("tidyverse", version = "2.0.0")'
 Rscript -e 'remotes::install_cran("ggbeeswarm", upgrade="never", version="0.6.1")'
 Rscript -e 'remotes::install_cran("gridExtra",upgrade="never", version = "2.3")'
 Rscript -e 'remotes::install_cran("rmarkdown",upgrade="never", version = "2.17")'

Dockerfile

@@ -1,5 +1,5 @@
 FROM rocker/r-ubuntu:22.04
-RUN apt-get update && apt-get install -y --no-install-recommends build-essential python3-pip libssl-dev libbz2-dev libsdl1.2-dev liblzma-dev libcurl4-openssl-dev zlib1g-dev libxml2-dev r-cran-tidyverse trf bwa bcftools samtools default-jre && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y --no-install-recommends build-essential python3-pip libssl-dev libbz2-dev libsdl1.2-dev liblzma-dev libcurl4-openssl-dev zlib1g-dev libxml2-dev trf bwa bcftools samtools default-jre pandoc && rm -rf /var/lib/apt/lists/*
 RUN pip install cutadapt==4.1
 
 RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
@@ -8,6 +8,7 @@ RUN R -e 'install.packages("remotes")'
 
 # Update apt-get
 RUN Rscript -e 'install.packages("remotes", version = "2.4.2")'
+RUN Rscript -e 'remotes::install_cran("tidyverse", version = "2.0.0")'
 RUN Rscript -e 'remotes::install_cran("ggbeeswarm", upgrade="never", version="0.6.1")'
 RUN Rscript -e 'remotes::install_cran("gridExtra",upgrade="never", version = "2.3")'
 RUN Rscript -e 'remotes::install_cran("rmarkdown",upgrade="never", version = "2.17")'

R_code/dada_overlaps.R

@@ -12,7 +12,6 @@ parser$add_argument('--band-size', type='integer', default=16)
 parser$add_argument('--omega-a', type='double', default=1e-120)
 parser$add_argument('--concat-non-overlaps', action='store_true')
 parser$add_argument('--use-quals', type="character", default="false")
-parser$add_argument('--homop-gap-penalty', type='integer') # null if not set, which is the default for dada2
 parser$add_argument('--maxEE', type="integer", default=2)
 
 
@@ -61,16 +60,14 @@ pool=switch(
   "pseudo" = "pseudo"
 )
 
-use_quals=switch(
-  args$use_quals,
-  "true" = TRUE,
-  "false" = FALSE
-)
-
-homop_gap_penalty <- ifelse(args$homop_gap_penalty <= 0, NULL, args$homop_gap_penalty)
+# use_quals=switch(
+#   args$use_quals,
+#   "true" = TRUE,
+#   "false" = FALSE
+# )
 
-dadaFs <- dada(derepFs, err=errF, selfConsist=TRUE, multithread=TRUE, verbose=TRUE, pool=pool, BAND_SIZE=args$band_size, OMEGA_A=args$omega_a, USE_QUALS=use_quals, HOMOPOLYMER_GAP_PENALTY=homop_gap_penalty)
-dadaRs <- dada(derepRs, err=errR, selfConsist=TRUE, multithread=TRUE, verbose=TRUE, pool=pool, BAND_SIZE=args$band_size, OMEGA_A=args$omega_a, USE_QUALS=use_quals, HOMOPOLYMER_GAP_PENALTY=homop_gap_penalty)
+dadaFs <- dada(derepFs, err=errF, selfConsist=TRUE, multithread=TRUE, verbose=TRUE, pool=pool, BAND_SIZE=args$band_size, OMEGA_A=args$omega_a)
+dadaRs <- dada(derepRs, err=errR, selfConsist=TRUE, multithread=TRUE, verbose=TRUE, pool=pool, BAND_SIZE=args$band_size, OMEGA_A=args$omega_a)
 
 if(args$concat_non_overlaps){