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Merge pull request #29 from IARCbioinfo/dev
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‎.circleci/config.yml

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- run: cd ~/project/ ; docker build -t iarcbioinfo/alignment-nf .
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- run: cd ; nextflow run ~/project/alignment.nf --help
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- run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_folder ~/data_test/BAM/ --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --cpu 2 --mem 4 -with-dag dag.png
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- run: cd ; echo -e "file1,RG1,$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz,$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2,RG1,$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz,$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz" > input.txt ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --cpu 2 --mem 4
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- run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000_nochr.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000_nochr.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4 -with-dag dag.png
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- run: cd ; echo -e "file1,RG1,$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz,$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2,RG1,$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz,$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2,RG2,$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz,$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz" > input_multiplex.txt ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --cpu 2 --mem 4
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- run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000_nochr.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000_nochr.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4 -with-dag dag.png
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- run: cd ; echo -e "SM\tRG\tpair1\tpair2\nfile1\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz" > input.txt ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --cpu 2 --mem 4
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- run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000_nochr.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000_nochr.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4
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- run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000_nochr.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000_nochr.vcf.gz --trim --adapterremoval_opt "--qualitymax 93" --cpu 2 --mem 4 --mem_BQSR 4
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- run: cd ; echo -e "SM\tRG\tpair1\tpair2\nfile1\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2\tRG2\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz" > input_multiplex.txt ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --cpu 2 --mem 4
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- run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000_nochr.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000_nochr.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4 -with-dag alignment-nf_dag.png
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- run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000_nochr.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000_nochr.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4 -with-dag alignment-nf_dag.html
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- run: cd ; cp ~/results/nf-pipeline_info/alignment-nf_dag.html ~/project/dag.html
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- deploy:
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branch: [master, dev]
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command: chmod +x deploy.sh && ./deploy.sh
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command: chmod +x deploy.sh && ./deploy.sh

‎Dockerfile

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################## BASE IMAGE #####################
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FROM nfcore/base
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FROM continuumio/miniconda3:4.7.12
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################## METADATA #######################
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LABEL base_image="nfcore/base"
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LABEL version="1.0"
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LABEL base_image="continuumio/miniconda3"
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LABEL version="4.7.12"
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LABEL software="alignment-nf"
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LABEL software.version="2.0"
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LABEL software.version="1.1"
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LABEL about.summary="Container image containing all requirements for alignment-nf"
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LABEL about.home="http://github.com/IARCbioinfo/alignment-nf"
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LABEL about.documentation="http://github.com/IARCbioinfo/alignment-nf/README.md"
@@ -21,75 +20,7 @@ MAINTAINER **nalcala** <**[email protected]**>
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################## INSTALLATION ######################
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COPY environment.yml /
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RUN conda env update -n root -f /environment.yml && conda clean -a
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RUN apt-get update && apt-get install -y procps && apt-get clean -y
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RUN conda env create -n alignment-nf -f /environment.yml && conda clean -a
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RUN ln -s /opt/conda/pkgs/bwakit-0.7.15-1/share/bwakit-0.7.15-1/k8 /usr/local/bin/.
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#RUN mkdir -p /var/cache/apt/archives/partial && \
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# touch /var/cache/apt/archives/lock && \
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# chmod 640 /var/cache/apt/archives/lock && \
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# apt-key adv --keyserver keyserver.ubuntu.com --recv-keys F76221572C52609D && \
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# apt-get clean && \
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# apt-get update -y && \
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# Install dependences
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# DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
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# make \
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# g++ \
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# zlib1g-dev \
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# libncurses5-dev \
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# git \
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# wget \
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# ca-certificates \
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# openjdk-6-jre \
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# bzip2 && \
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# Install miniconda
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# wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
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# chmod 755 Miniconda3-latest-Linux-x86_64.sh && \
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# ./Miniconda3-latest-Linux-x86_64.sh && \
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# Install samtools specific version manually
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# wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
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# tar -jxf samtools-1.3.1.tar.bz2 && \
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# cd samtools-1.3.1 && \
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# make && \
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# make install && \
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# cd .. && \
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# rm -rf samtools-1.3.1 samtools-1.3.1.tar.bz2 && \
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# Install bwa specific version manually
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# wget https://github.com/lh3/bwa/releases/download/v0.7.15/bwakit-0.7.15_x64-linux.tar.bz2 && \
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# tar -jxf bwakit-0.7.15_x64-linux.tar.bz2 && \
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# cp bwa.kit/bwa* /usr/local/bin/. && \
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# cp bwa.kit/k8 /usr/local/bin/. && \
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# cp bwa.kit/typeHLA* /usr/local/bin/. && \
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# rm -rf bwakit-0.7.15_x64-linux.tar.bz2 bwa.kit && \
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# Install samblaster specific version manually
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# wget https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.24/samblaster-v.0.1.24.tar.gz && \
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# tar -xzf samblaster-v.0.1.24.tar.gz && \
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# cd samblaster-v.0.1.24 && \
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# make && \
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# cp samblaster /usr/local/bin/. && \
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# cd .. && \
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# rm -rf samblaster-v.0.1.24.tar.gz samblaster-v.0.1.24 && \
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# Install sambamba specific version manually
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# wget https://github.com/lomereiter/sambamba/releases/download/v0.6.6/sambamba_v0.6.6_linux.tar.bz2 && \
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# tar -jxf sambamba_v0.6.6_linux.tar.bz2 && \
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# cp sambamba_v0.6.6 /usr/local/bin/sambamba && \
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# rm -rf sambamba_v0.6.6_linux.tar.bz2 && \
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# Remove unnecessary dependences
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# DEBIAN_FRONTEND=noninteractive apt-get remove -y \
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# make \
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# g++ \
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# zlib1g-dev \
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# libncurses5-dev \
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# git \
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# wget \
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# ca-certificates \
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# bzip2 && \
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# Clean
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# DEBIAN_FRONTEND=noninteractive apt-get autoremove -y && \
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# apt-get clean
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ENV PATH /opt/conda/envs/alignment-nf/bin:$PATH

‎Singularity/Singularity.v1.1

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From:iarcbioinfo/alignment-nf:v1.1
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Bootstrap:docker
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%labels
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MAINTAINER **alcalan** <**[email protected]**>
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DESCRIPTION Container image containing all requirements for pipeline alignment-nf
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VERSION 1.1

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