Merge branch 'master' of gitbio.ens-lyon.fr:pipelines/nextflow

src/.conda_envs/bwa_0.7.17

+/Xnfs/lbmcdb/common/conda/envs/bwa_0.7.17
\ No newline at end of file

src/.conda_envs/gatk_3.8.0

+/Xnfs/lbmcdb/common/conda/envs/gatk_3.8.0
\ No newline at end of file

src/.conda_envs/last_1060

+/Xnfs/lbmcdb/common/conda/envs/last_1060
\ No newline at end of file

src/.conda_packages.sh

@@ -45,6 +45,9 @@ fi
 if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
   conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
 fi
+if [ ! -d ${CONDA_ENVS}bwa_0.7.17 ]; then
+  conda create --yes --name bwa_0.7.17 -c bioconda bwa=0.7.17
+fi
 if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
   conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
 fi

src/.docker_modules/gatk/3.8.0/Dockerfile

@@ -2,3 +2,6 @@ FROM broadinstitute/gatk3:3.8-0
 MAINTAINER Laurent Modolo
 
 ENV GATK_VERSION=3.8.0
+
+RUN echo "#\!/bin/sh\njava -jar /usr/GenomeAnalysisTK.jar \$@" > /bin/gatk3 
+RUN chmod +x /bin/gatk3

src/.docker_modules/htseq/0.11.2/Dockerfile

-
 FROM ubuntu:18.04
 MAINTAINER Laurent Modolo
 
 ENV HTSEQ_VERSION=0.11.2
-ENV PACKAGES build-essential \
-             python3-pip \
-             python3-setuptools \
-             python3-dev \
-             python3-wheel
+ENV PACKAGES build-essential=12.4* \
+             python3-pip=9.0.1* \
+             python3-setuptools=39.0.1* \
+             python3-dev=3.6.7* \
+             python3-wheel=0.30.0*
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \

src/.docker_modules/htseq/0.11.2/docker_init.sh

 #!/bin/sh
-docker pull lbmc/htseq:0.11.2
-docker build src/.docker_modules/htseq/0.11.2 -t 'lbmc/htseq:0.11.2'
-docker push lbmc/htseq:0.11.2
+docker build src/docker_modules/HTSeq/0.11.2 -t 'htseq:0.11.2'

src/.docker_modules/last/1060/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV LAST_VERSION=1060
+ENV PACKAGES curl=7.58.0* \
+    unzip \
+    make=4.1* \
+    g++ \
+    zlib1g-dev=1:1.2.11* \
+    ca-certificates=20180409 \
+    build-essential=12.4*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L http://last.cbrc.jp/last-${LAST_VERSION}.zip -o last-${LAST_VERSION}.zip && \
+unzip last-${LAST_VERSION}.zip && \
+cd last-${LAST_VERSION} && \
+make && \
+cp src/last* /usr/bin/ && \
+cp scripts/* /usr/bin/ && \
+cd .. && \
+rm -Rf last-${LAST_VERSION}

src/.docker_modules/last/1060/docker_init.sh

+#!/bin/sh
+docker pull lbmc/last:1060
+docker build src/.docker_modules/last/1060/ -t 'lbmc/last:1060'
+docker push lbmc/last:1060

src/.docker_modules/picard/2.18.11/PicardCommandLine

@@ -12,4 +12,4 @@ PicardCommandLine)
         ;;
 esac
 
-exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
+exec java -Xmx12g ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"

src/nf_modules/kallisto/indexing.config

@@ -3,7 +3,7 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withNamek index_fasta {
+      withName index_fasta {
         container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }