upgrade modules and moving to different containers

TODO.md

@@ -1,6 +1,7 @@
 - Moving modules into modules folder
 - Adding nextflow_schema.json
 - Review container
-
-* Testing new DSL2 version against old one
-* Move parts into subworkflows for clarity if possible
+- Testing new DSL2 version against old one
+- Move parts into subworkflows for clarity if possible
+- Convert params.config to params.yaml
+- Include colors into the terminal messages

bin/B0_generate_IPA_prot_aln.pl

@@ -17,7 +17,7 @@
 
 ### with clustal
 if ($aligner=~/clustal/i){
-    system "clustalw2 $exint -output=gde";
+    system "clustalw $exint -output=gde";
 }
 elsif ($aligner=~/MAFFT/i){
     system "mafft --auto --thread $cpus --quiet $exint | sed 's/>/%/g' > $root.gde";  

docker/Rscript/Dockerfile

@@ -1,6 +1,6 @@
 FROM rocker/r-ver:3.6.3
 
-RUN apt-get -y update && apt-get install -y libnlopt-dev \
+RUN apt-get -y update && apt-get install -y libnlopt-dev libxml2-dev libcurl4-openssl-dev \
   && rm -rf /var/lib/apt/lists/*
 
 COPY deps.R /tmp

docker/Rscript/deps.R

@@ -1,8 +1,8 @@
 install.packages('devtools', dependencies=TRUE, repos='cran.rstudio.com/');
+require(devtools)
 install.packages(c('igraph'), repos='http://cran.us.r-project.org');
 install.packages(c('ggplot2'), repos='http://cran.us.r-project.org');
 install.packages(c('nloptr'), repos='http://cran.us.r-project.org');
 install.packages(c('pbkrtest', 'lme4', 'pbkrtest', 'lme4'), repos='http://cran.us.r-project.org');
 install.packages(c('ggpubr', 'cowplot'), repos='http://cran.us.r-project.org');
-install.packages(c('hashmap'), repos='http://cran.us.r-project.org');
-
+devtools::install_github('nathan-russell/hashmap')

docker/aligners/Dockerfile

@@ -0,0 +1,16 @@
+FROM perl:5.24-threaded-buster
+
+ARG MAFFT_VERSION=7.429
+
+RUN apt-get update -y && apt-get install -y build-essential clustalw && rm -rf /var/lib/apt/lists/*
+
+#Installing MAFFT
+WORKDIR /tmp
+RUN curl -k -L https://mafft.cbrc.jp/alignment/software/mafft-${MAFFT_VERSION}-with-extensions-src.tgz > mafft.tgz
+RUN tar -zvxf mafft.tgz
+RUN cd mafft-${MAFFT_VERSION}-with-extensions/core;make clean; make; make install; cd ../../; rm mafft.tgz
+
+WORKDIR /
+
+# ENV LC_ALL=en_US.UTF8
+# ENV LANG=en_US.UTF8

modules/local/exorthist/align_pairs.nf

@@ -1,6 +1,6 @@
 process PARSE_IPA_PROT_ALN {
     tag { cls_part_file.name }
-    label 'big_cpus'
+    label 'aligners'
 
     input:
     path blosumfile

nextflow.config

@@ -25,11 +25,6 @@ process {
     scratch = false
     containerOptions = { workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g)': null}
 
-    withLabel: big_cpus {
-        cpus = 2
-        memory = '5G'
-    }
-
     withLabel: incr_time_cpus {
        errorStrategy = 'retry'
        memory = '5G'
@@ -52,14 +47,21 @@ process {
      container = 'quay.io/biocontainers/pandas:1.5.2'
     }
 
+    withLabel: aligners {
+      cpus = 2
+      memory = '5G'
+      container = 'biocorecrg/exorthist_aligners:2.0.0'
+    }
+
     withLabel: rscript {
-     container = 'rocker/r-ver:3.6.3'
+     container = 'biocorecrg/exorthist_rscript:2.0.0'
     }
 
 
 }
 
-process.container = 'biocorecrg/exon_intron_pipe:0.2'
+// process.container = 'biocorecrg/exon_intron_pipe:0.2'
+process.container = 'perl:5.24-threaded-buster'
 //singularity.enabled = true
 singularity.cacheDir = "$baseDir/singularity"