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Merge pull request #91 from nf-core/dev
Bump versions to 1.1.0
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‎.github/workflows/ci.yml‎

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name: nf-core CI
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# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
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on:
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push:
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branches:
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- dev
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pull_request:
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release:
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types: [published]
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jobs:
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test:
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name: Run workflow tests
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# Only run on push if this is the nf-core dev branch (merged PRs)
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: ${{ matrix.nxf_ver }}
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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# Nextflow versions: check pipeline minimum and current latest
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nxf_ver: ['19.10.0', '']
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v1
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with:
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PREFIX_FILTER: |
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Dockerfile
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environment.yml
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- name: Build new docker image
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if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:dev
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with test data
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker
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profile:
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name: Run profile tests
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: '19.10.0'
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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profiles: [test_bc_nodx, test_nobc_dx, test_nobc_nodx, test_nobc_nodx_noaln]
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v1
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with:
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PREFIX_FILTER: |
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Dockerfile
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environment.yml
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- name: Build new docker image
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if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:dev
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with different profiles
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profiles }},docker
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parameters:
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name: Run parameter tests
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: '19.10.0'
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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parameters: [--aligner graphmap2, --skip_alignment, --skip_qc, --skip_quantification]
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v1
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with:
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PREFIX_FILTER: |
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Dockerfile
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environment.yml
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- name: Build new docker image
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if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:dev
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with different parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
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quantification:
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name: Run quantification tests
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: '19.10.0'
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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parameters: [--quantification_method 'stringtie2', --skip_quantification, --skip_differential_analysis]
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v1
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with:
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PREFIX_FILTER: |
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Dockerfile
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environment.yml
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- name: Build new docker image
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if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:dev
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:dev
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with different quantification parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_nobc_nodx,docker ${{ matrix.parameters }}
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name: nf-core CI
2+
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
3+
on:
4+
push:
5+
branches:
6+
- dev
7+
pull_request:
8+
release:
9+
types: [published]
10+
11+
jobs:
12+
test:
13+
name: Run workflow tests
14+
# Only run on push if this is the nf-core dev branch (merged PRs)
15+
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: ${{ matrix.nxf_ver }}
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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# Nextflow versions: check pipeline minimum and current latest
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nxf_ver: ['19.10.0', '']
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
27+
28+
- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v1
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with:
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PREFIX_FILTER: |
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Dockerfile
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environment.yml
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- name: Build new docker image
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if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
49+
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- name: Run pipeline with test data
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker
53+
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profile:
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name: Run profile tests
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
57+
runs-on: ubuntu-latest
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env:
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NXF_VER: '19.10.0'
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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profiles: [test_bc_nodx, test_nobc_dx, test_nobc_nodx, test_nobc_nodx_noaln]
64+
steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
67+
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v1
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with:
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PREFIX_FILTER: |
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Dockerfile
73+
environment.yml
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- name: Build new docker image
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if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with different profiles
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profiles }},docker
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parameters:
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name: Run parameter tests
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: '19.10.0'
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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parameters: [--aligner graphmap2, --skip_alignment, --skip_qc, --skip_quantification]
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steps:
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- name: Check out pipeline code
106+
uses: actions/checkout@v2
107+
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- name: Check if Dockerfile or Conda environment changed
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uses: technote-space/get-diff-action@v1
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with:
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PREFIX_FILTER: |
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Dockerfile
113+
environment.yml
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- name: Build new docker image
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if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with different parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
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quantification:
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name: Run quantification tests
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: '19.10.0'
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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parameters: [--quantification_method 'stringtie2', --skip_quantification, --skip_differential_analysis]
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steps:
145+
- name: Check out pipeline code
146+
uses: actions/checkout@v2
147+
148+
- name: Check if Dockerfile or Conda environment changed
149+
uses: technote-space/get-diff-action@v1
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with:
151+
PREFIX_FILTER: |
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Dockerfile
153+
environment.yml
154+
155+
- name: Build new docker image
156+
if: env.GIT_DIFF
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run: docker build --no-cache . -t nfcore/nanoseq:1.1.0
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- name: Pull docker image
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if: ${{ !env.GIT_DIFF }}
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run: |
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docker pull nfcore/nanoseq:dev
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docker tag nfcore/nanoseq:dev nfcore/nanoseq:1.1.0
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with different quantification parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_nobc_nodx,docker ${{ matrix.parameters }}

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [1.1.0] - 2020-11-13
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## [1.1.0] - 2020-11-06
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### Major enhancements
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‎Dockerfile‎

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RUN conda env create --quiet -f /environment.yml && conda clean -a
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# Add conda installation dir to PATH (instead of doing 'conda activate')
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ENV PATH /opt/conda/envs/nf-core-nanoseq-1.1.0dev/bin:$PATH
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ENV PATH /opt/conda/envs/nf-core-nanoseq-1.1.0/bin:$PATH
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# Dump the details of the installed packages to a file for posterity
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RUN conda env export --name nf-core-nanoseq-1.1.0dev > nf-core-nanoseq-1.1.0dev.yml
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RUN conda env export --name nf-core-nanoseq-1.1.0 > nf-core-nanoseq-1.1.0.yml
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# Instruct R processes to use these empty files instead of clashing with a local version
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RUN touch .Rprofile

‎environment.yml‎

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# You can use this file to create a conda environment for this pipeline:
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# conda env create -f environment.yml
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name: nf-core-nanoseq-1.1.0dev
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name: nf-core-nanoseq-1.1.0
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channels:
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- conda-forge
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- bioconda

‎main.nf‎

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@@ -1011,7 +1011,7 @@ if (!params.skip_quantification && (params.protocol == 'cDNA' || params.protocol
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* Quantification and novel isoform detection with bambu
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*/
10131013
process BAMBU {
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label 'process_medium'
1014+
label 'process_high'
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publishDir "${params.outdir}/${params.quantification_method}", mode: params.publish_dir_mode,
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saveAs: { filename ->
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if (!filename.endsWith("bambu.txt")) filename

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