Merge pull request #30 from luslab/dev

      - name: Run pipeline with test data

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile test_no_igg,docker

# ---------------------------------------------------------------------

  test_all_exp_one_igg_small:

    name: Run pipeline test with 2 groups of 2 replicate and one replicate of igg

    # Only run on push if this is the luslab dev branch (merged PRs)

    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}

    runs-on: ubuntu-latest

    env:

      NXF_VER: ${{ matrix.nxf_ver }}

      NXF_ANSI_LOG: false

    strategy:

      matrix:

        # Nextflow versions: check pipeline minimum and current latest

        nxf_ver: ["21.04.0", ""]

    steps:

      - name: Check out pipeline code

        uses: actions/checkout@v2

      - name: Install Nextflow

        run: |

          wget -qO- get.nextflow.io | bash

          sudo mv nextflow /usr/local/bin/

      - name: Run pipeline with test data

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile test_all_exp_one_igg_small,docker --skip_deseq2

# ---------------------------------------------------------------------

  test_one_exp_all_igg_small:

    name: Run pipeline test with 2 groups of 2 replicate and one replicate of igg

    # Only run on push if this is the luslab dev branch (merged PRs)

    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}

    runs-on: ubuntu-latest

    env:

      NXF_VER: ${{ matrix.nxf_ver }}

      NXF_ANSI_LOG: false

    strategy:

      matrix:

        # Nextflow versions: check pipeline minimum and current latest

        nxf_ver: ["21.04.0", ""]

    steps:

      - name: Check out pipeline code

        uses: actions/checkout@v2

      - name: Install Nextflow

        run: |

          wget -qO- get.nextflow.io | bash

          sudo mv nextflow /usr/local/bin/

      - name: Run pipeline with test data

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile test_one_exp_all_igg_small,docker --skip_deseq2

data/

results/

.DS_Store

tests/

testing/

testing*

*.pyc

dev/docker/static_reports/test_output/*

!dev/docker/static_reports/test_data/_dummy.txt

!dev/docker/static_reports/test_output/_dummy.txt

!tests/data/

[![GitHub Actions Linting Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/cutandrun/actions)

[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A521.04.0-brightgreen.svg)](https://www.nextflow.io/)

[![Docker](https://img.shields.io/docker/automated/nfcore/cutandrun.svg)](https://hub.docker.com/r/nfcore/cutandrun)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23cutandrun-4A154B?logo=slack)](https://nfcore.slack.com/channels/cutandrun)

## Introduction

id: 'fragment_lengths'

section_name: 'Fragment Length Distribution'

description: "Fragment length distribution QC"

plot_type: 'linegraph'

anchor: 'fragment_lengths'

pconfig:

    title: 'Fragment Length Distribution Plot'

    xlab: Length (bp)

    ylab: Frequency

report_header_info:

  - Contact E-mail: "chris.cheshire@crick.ac.uk"

  - Application Type: "CUT&TAG"

  - Application Type: "CUT&RUN"

  - Project Type: "Application"

  - Sequencing Platform: "HiSeq 2500 High Output V4"

  - Sequencing Setup: "2x50"

  # - Sequencing Platform: "HiSeq 2500 High Output V4"

  # - Sequencing Setup: "2x50"

show_analysis_paths: True

show_analysis_time: True

# show_analysis_paths: True

# show_analysis_time: True

show_hide_buttons:

  - Read Group 1

  - Read Group 2

  - Controls

  - Conditions

show_hide_mode:

  - show

  - show

  - show

  - show

show_hide_patterns:

  - _r1

  - _r2

  - igg_

  - ["h3k4me3_", "h3k27me3_"]

# show_hide_buttons:

#   - Read Group 1

#   - Read Group 2

#   - Controls

#   - Conditions

# show_hide_mode:

#   - show

#   - show

#   - show

#   - show

# show_hide_patterns:

#   - _r1

#   - _r2

#   - igg_

#   - ["h3k4me3_", "h3k27me3_"]

export_plots: true

# export_plots: true

# Run only these modules

run_modules:

    - picard

module_order:

    - custom_content

    - fastqc:

        name: 'FastQC (raw)'

        info: 'This section of the report shows FastQC results before adapter trimming.'

            - "./bowtie2/*spikein.bowtie2.log"

    - samtools

    - picard

    - custom_content

report_section_order:

    software_versions:

        - It can be due to the Tn5 preference.

        - What you might be detecting is the 10-bp periodicity that shows up as a sawtooth pattern in the length distribution. If so, this is normal and will not affect alignment or peak calling. In any case we do not recommend trimming as the bowtie2 parameters that we list will give accurate mapping information without trimming.

fastqc_config:

    fastqc_theoretical_gc: "hg38_genome"

# fastqc_config:

#     fastqc_theoretical_gc: "hg38_genome"

# extra_fn_clean_exts:

#   - ".spikein.bowtie2"

#   - "_processedFile"

# extra_fn_clean_trim:

#   - "#"

#   - ".myext"

# Customise the module search patterns to speed up execution time

#  - Skip module sub-tools that we are not interested in