Commit 9a363007 authored by Tamara Hodgetts's avatar Tamara Hodgetts
Browse files

Merge branch 'dev' into resource-allocation

parents 7e32a4cd 3aa35a91

.github/ISSUE_TEMPLATE/bug_report.yml

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name: Bug report

description: Report something that is broken or incorrect

labels: bug

.github/PULL_REQUEST_TEMPLATE.md

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@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/cuta 
    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)

    - [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.

- [ ] Make sure your code lints (`nf-core lint`).

- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).

- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).

- [ ] Usage Documentation in `docs/usage.md` is updated.

- [ ] Output Documentation in `docs/output.md` is updated.

- [ ] `CHANGELOG.md` is updated.

.github/workflows/awsfulltest.yml

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@@ -14,7 +14,7 @@ jobs: 
    runs-on: ubuntu-latest

    steps:

      - name: Launch workflow via tower

        uses: nf-core/tower-action@v2

        uses: nf-core/tower-action@v3

        # TODO nf-core: You can customise AWS full pipeline tests as required

        # Add full size test data (but still relatively small datasets for few samples)

        # on the `test_full.config` test runs with only one set of parameters
@@ -31,4 +31,6 @@ jobs: 
              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"

            }

          profiles: test_full,aws_tower

          pre_run_script: 'export NXF_VER=21.10.3'
 
          nextflow_config: |

            process.errorStrategy = 'retry'

            process.maxRetries = 3

.github/workflows/awstest.yml

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@@ -11,7 +11,7 @@ jobs: 
    runs-on: ubuntu-latest

    steps:

      - name: Launch workflow via tower

        uses: nf-core/tower-action@v2

        uses: nf-core/tower-action@v3

        

        with:

          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -25,4 +25,6 @@ jobs: 
              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-test-${{ github.sha }}"

            }

          profiles: test,aws_tower

          pre_run_script: 'export NXF_VER=21.10.3'
 
          nextflow_config: |

            process.errorStrategy = 'retry'

            process.maxRetries = 3

.github/workflows/ci.yml

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@@ -49,9 +49,11 @@ jobs: 
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz



      - name: Run pipeline

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

      - name: Run Pipeline

        uses: Wandalen/wretry.action@v1.0.11

        with:

          command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

          attempt_limit: 2



  ##############################

  ### LARGE INTEGRATION TEST ###
@@ -89,9 +91,11 @@ jobs: 
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz



      - name: Run pipeline with test data

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip

      - name: Run Pipeline

        uses: Wandalen/wretry.action@v1.0.11

        with:

          command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip

          attempt_limit: 2



  #####################################

  ### EDGE VERSION INTEGRATION TEST ###
@@ -127,9 +131,11 @@ jobs: 
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz



      - name: Run pipeline with test data

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

      - name: Run Pipeline

        uses: Wandalen/wretry.action@v1.0.11

        with:

          command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

          attempt_limit: 2



  ##############################

  ###      UNIT TESTS        ###
@@ -163,39 +169,53 @@ jobs: 
          - verify_output_align_duplicates_remove

          - verify_output_align_duplicates_remove_target

          - verify_output_peak_calling_only_peak_calling

          - test_peak_callers

          - test_bam_scale_none

          - test_bam_scale_spikein

          - test_bam_scale_cpm

          - test_bam_scale_rpkm

          - test_bam_scale_bpm

          - test_bam_scale_cpm_iggscale

          - test_peak_callers_seacr

          - test_peak_callers_macs2

          - test_peak_callers_invalid

          - test_peak_callers_seacr_macs2

          - test_peak_callers_macs2_seacr

          - test_peak_callers_seacr_macs2_noigg

          - test_conseneus_peaks_group

          - test_conseneus_peaks_all

          - test_conseneus_peaks_invalid

          - verify_output_reporting

          - verify_output_reporting_skip_reporting

          - verify_output_reporting_skip_igv

          - verify_output_reporting_skip_heatmaps

          - verify_output_reporting_skip_multiqc

    steps:

      - uses: actions/checkout@v2

      - name: Checkout Code

        uses: actions/checkout@v2



      - name: Set up Python

        uses: actions/setup-python@v2

        with:

          python-version: "3.x"



      - uses: actions/cache@v2

      - name: Setup Pip Cache

        uses: actions/cache@v2

        with:

          path: ~/.cache/pip

          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}

          restore-keys: |

            ${{ runner.os }}-pip-

      - name: Set up Python

        uses: actions/setup-python@v2

        with:

          python-version: "3.x"



      - name: Install Python dependencies

        run: python -m pip install --upgrade pip pytest-workflow



      - uses: actions/cache@v2

      - name: Restore Keys

        uses: actions/cache@v2

        with:

          path: /usr/local/bin/nextflow

          key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}

          restore-keys: |

            ${{ runner.os }}-nextflow-



      - name: Install Nextflow

        env:

          NXF_VER: ${{ matrix.nxf_version }}
@@ -203,8 +223,12 @@ jobs: 
        run: |

          wget -qO- get.nextflow.io | bash

          sudo mv nextflow /usr/local/bin/



      - name: Run pytest-workflow

        run: pytest --tag ${{ matrix.tags }} --kwdof

        uses: Wandalen/wretry.action@v1.0.11

        with:

          command: pytest --tag ${{ matrix.tags }} --kwdof

          attempt_limit: 3



      - name: Upload logs on failure

        if: failure()

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