CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
69 lines
2.4 KiB
YAML
69 lines
2.4 KiB
YAML
name: "preseq_lcextrap"
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info:
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migration_info:
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git_repo: https://github.com/nf-core/rnaseq.git
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paths: [modules/nf-core/preseq/lcextrap/main.nf, modules/nf-core/preseq/lcextrap/meta.yml]
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last_sha: 54721c6946daf6d602d7069dc127deef9cbe6b33
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description: Computing the expected future yield of distinct reads and bounds on the number of total distinct reads in the library and the associated confidence intervals.
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argument_groups:
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- name: "Input"
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arguments:
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- name: "--input"
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type: file
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description: Input genome BAM/BED file
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- name: "--extra_preseq_args"
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type: string
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- name: "--paired"
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type: boolean
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description: Paired-end reads?
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- name: "Output"
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arguments:
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- name: "--output"
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type: file
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direction: output
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default: $id.lc_extrap.txt
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resources:
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- type: bash_script
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path: script.sh
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test_resources:
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- type: bash_script
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path: test.sh
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- path: /testData/unit_test_resources/a.sorted.bed
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- path: /testData/unit_test_resources/SRR1106616_5M_subset.bam
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engines:
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- type: docker
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image: ubuntu:22.04
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setup:
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- type: apt
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packages: [ curl, bzip2, build-essential, wget, gcc, autoconf, automake, make, libz-dev, libbz2-dev, zlib1g-dev, libncurses5-dev, libncursesw5-dev, liblzma-dev, pip ]
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- type: docker
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run: |
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cd /usr/bin && \
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wget --no-check-certificate https://github.com/smithlabcode/preseq/releases/download/v3.2.0/preseq-3.2.0.tar.gz && \
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wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && \
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wget --no-check-certificate https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static && \
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curl -fsSL https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 -o samtools-1.18.tar.bz2 && \
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tar -xjf samtools-1.18.tar.bz2 && rm samtools-1.18.tar.bz2 && \
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tar -xzf preseq-3.2.0.tar.gz && rm preseq-3.2.0.tar.gz && \
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tar -vxjf htslib-1.9.tar.bz2 && rm htslib-1.9.tar.bz2 && \
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mv bedtools.static /usr/local/bin/bedtools && \
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chmod a+x /usr/local/bin/bedtools && \
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cd samtools-1.18 && \
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./configure && \
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make && \
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make install && \
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cd /usr/bin && cd htslib-1.9 && \
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make && \
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cd /usr/bin && cd preseq-3.2.0 && \
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mkdir build && cd build && \
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../configure && \
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make && make install && make HAVE_HTSLIB=1 all
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runners:
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- type: executable
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- type: nextflow
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