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Merge pull request #171 from nf-core/patch
Update schema to use new definitions groups
2 parents 048fd68 + 2bf81d0 commit 0f487ed

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‎.github/workflows/ci.yml

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@@ -35,13 +35,13 @@ jobs:
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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/chipseq:1.2.0
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run: docker build --no-cache . -t nfcore/chipseq:1.2.1
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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/chipseq:dev
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docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0
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docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.1
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- name: Install Nextflow
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run: |
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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/chipseq:1.2.0
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run: docker build --no-cache . -t nfcore/chipseq:1.2.1
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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/chipseq:dev
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docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0
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docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.1
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- name: Install Nextflow
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run: |

‎CHANGELOG.md

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@@ -3,6 +3,10 @@
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The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
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## [1.2.1] - 2020-07-29
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* [#171](https://github.com/nf-core/chipseq/issues/171) - Minor patch release to update pipeline schema
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## [1.2.0] - 2020-07-02
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### `Added`

‎Dockerfile

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@@ -7,10 +7,10 @@ COPY environment.yml /
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RUN conda env create -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-chipseq-1.2.0/bin:$PATH
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ENV PATH /opt/conda/envs/nf-core-chipseq-1.2.1/bin:$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-chipseq-1.2.0 > nf-core-chipseq-1.2.0.yml
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RUN conda env export --name nf-core-chipseq-1.2.1 > nf-core-chipseq-1.2.1.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-chipseq-1.2.0
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name: nf-core-chipseq-1.2.1
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channels:
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- conda-forge
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- bioconda

‎nextflow.config

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@@ -96,7 +96,7 @@ params {
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// Container slug. Stable releases should specify release tag!
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// Developmental code should specify :dev
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process.container = 'nfcore/chipseq:1.2.0'
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process.container = 'nfcore/chipseq:1.2.1'
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// Load base.config by default for all pipelines
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includeConfig 'conf/base.config'
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description = 'ChIP-seq peak-calling and differential analysis pipeline.'
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mainScript = 'main.nf'
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nextflowVersion = '>=19.10.0'
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version = '1.2.0'
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version = '1.2.1'
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}
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// Function to ensure that resource requirements don't go beyond

‎nextflow_schema.json

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{
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"$schema": "http://json-schema.org/draft-07/schema",
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"$id": "https://raw.githubusercontent.com/nf-core/atacseq/master/nextflow_schema.json",
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"title": "nf-core/atacseq pipeline parameters",
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"description": "ATACSeq peak-calling and differential analysis pipeline.",
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"$schema": "https://json-schema.org/draft-07/schema",
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"$id": "https://raw.githubusercontent.com/nf-core/chipseq/master/nextflow_schema.json",
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"title": "nf-core/chipseq pipeline parameters",
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"description": "ChIP-seq peak-calling and differential analysis pipeline.",
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"type": "object",
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"properties": {
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"Input/output options": {
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"definitions": {
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"input_output_options": {
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"title": "Input/output options",
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"type": "object",
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"properties": {
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"input": {
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"type": "string",
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"description": "Path to comma-separated file containing information about the samples in the experiment.",
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"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/atacseq/docs/usage#--input).",
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"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/chipseq/docs/usage#--input).",
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"fa_icon": "fas fa-file-csv"
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},
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"single_end": {
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],
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"fa_icon": "fas fa-terminal"
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},
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"Reference genome options": {
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"reference_genome_options": {
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"title": "Reference genome options",
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"type": "object",
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"properties": {
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"genome": {
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},
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"fa_icon": "fas fa-dna"
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},
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"Adapter trimming options": {
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"adapter_trimming_options": {
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"title": "Adapter trimming options",
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"type": "object",
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"properties": {
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"clip_r1": {
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"default": false,
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"description": "Skip the adapter trimming step.",
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"help_text": "Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"save_trimmed": {
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"type": "boolean",
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},
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"fa_icon": "fas fa-cut"
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},
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"Alignment options": {
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"alignment_options": {
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"title": "Alignment options",
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"type": "object",
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"properties": {
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"keep_dups": {
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},
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"fa_icon": "fas fa-map-signs"
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},
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"Peak calling options": {
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"peak_calling_options": {
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"title": "Peak calling options",
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"type": "object",
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"properties": {
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"narrow_peak": {
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},
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"skip_peak_qc": {
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"type": "boolean",
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"fa_icon": "fas fa-forward",
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"fa_icon": "fas fa-fast-forward",
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"description": "Skip MACS2 peak QC plot generation.",
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"default": false
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},
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"skip_peak_annotation": {
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"type": "boolean",
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"fa_icon": "fas fa-forward",
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"fa_icon": "fas fa-fast-forward",
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"description": "Skip annotation of MACS2 and consensus peaks with HOMER.",
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"default": false
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},
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"skip_consensus_peaks": {
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"type": "boolean",
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"default": false,
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"description": "Skip consensus peak generation, annotation and counting.",
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"fa_icon": "fas fa-forward",
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"fa_icon": "fas fa-fast-forward",
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"help_text": ""
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}
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},
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"fa_icon": "fas fa-chart-area"
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},
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"Differential analysis options": {
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"differential_analysis_options": {
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"title": "Differential analysis options",
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"type": "object",
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"properties": {
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"deseq2_vst": {
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"type": "boolean",
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"default": false,
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"description": "Skip differential accessibility analysis.",
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"fa_icon": "fas fa-forward",
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"fa_icon": "fas fa-fast-forward",
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"help_text": ""
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}
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},
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"fa_icon": "fas fa-not-equal"
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},
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"Process skipping options": {
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"process_skipping_options": {
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"title": "Process skipping options",
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"type": "object",
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"properties": {
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"skip_fastqc": {
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"type": "boolean",
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"default": false,
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"description": "Skip FastQC.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"skip_picard_metrics": {
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"type": "boolean",
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"default": false,
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"description": "Skip Picard CollectMultipleMetrics.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"skip_preseq": {
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"type": "boolean",
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"default": false,
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"description": "Skip Preseq.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"skip_plot_profile": {
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"type": "boolean",
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"default": false,
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"description": "Skip deepTools plotProfile.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"skip_plot_fingerprint": {
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"type": "boolean",
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"default": false,
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"description": "Skip deepTools plotFingerprint.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"skip_spp": {
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"type": "boolean",
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"default": false,
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"description": "Skip Phantompeakqualtools.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"skip_igv": {
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"type": "boolean",
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"default": false,
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"description": "Skip IGV.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"skip_multiqc": {
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"type": "boolean",
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"default": false,
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"description": "Skip MultiQC.",
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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}
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},
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"fa_icon": "fas fa-forward"
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"fa_icon": "fas fa-fast-forward"
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},
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"Institutional config options": {
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"institutional_config_options": {
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"title": "Institutional config options",
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"type": "object",
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"properties": {
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"custom_config_version": {
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},
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"fa_icon": "fas fa-university"
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},
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"Max job request options": {
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"max_job_request_options": {
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"title": "Max job request options",
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"type": "object",
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"properties": {
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"max_cpus": {
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},
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"fa_icon": "fab fa-acquisitions-incorporated"
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},
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"Generic options": {
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"generic_options": {
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"title": "Generic options",
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"type": "object",
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"properties": {
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"help": {
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},
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"fa_icon": "fas fa-file-import"
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/input_output_options"
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},
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{
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"$ref": "#/definitions/reference_genome_options"
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},
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{
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"$ref": "#/definitions/adapter_trimming_options"
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},
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{
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"$ref": "#/definitions/alignment_options"
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},
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{
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"$ref": "#/definitions/peak_calling_options"
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},
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{
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"$ref": "#/definitions/differential_analysis_options"
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},
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{
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"$ref": "#/definitions/process_skipping_options"
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},
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{
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"$ref": "#/definitions/institutional_config_options"
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},
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{
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"$ref": "#/definitions/max_job_request_options"
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},
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{
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"$ref": "#/definitions/generic_options"
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}
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]
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}

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