From 4dc7508f5768a160a2b5d1e8f3791da0f65a2e47 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 28 Jul 2020 10:38:44 +0200 Subject: [PATCH 1/4] Bump-version 1.2.1 --- .github/workflows/ci.yml | 8 ++++---- Dockerfile | 4 ++-- environment.yml | 2 +- nextflow.config | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8a37ba68..bdf469a2 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,13 +35,13 @@ jobs: - name: Build new docker image if: env.GIT_DIFF - run: docker build --no-cache . -t nfcore/atacseq:1.2.0 + run: docker build --no-cache . -t nfcore/atacseq:1.2.1 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/atacseq:dev - docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.0 + docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.1 - name: Install Nextflow run: | @@ -75,13 +75,13 @@ jobs: - name: Build new docker image if: env.GIT_DIFF - run: docker build --no-cache . -t nfcore/atacseq:1.2.0 + run: docker build --no-cache . -t nfcore/atacseq:1.2.1 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/atacseq:dev - docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.0 + docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.1 - name: Install Nextflow run: | diff --git a/Dockerfile b/Dockerfile index 715e6892..bb346cc3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,10 +7,10 @@ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-atacseq-1.2.0/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-atacseq-1.2.1/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-atacseq-1.2.0 > nf-core-atacseq-1.2.0.yml +RUN conda env export --name nf-core-atacseq-1.2.1 > nf-core-atacseq-1.2.1.yml # Instruct R processes to use these empty files instead of clashing with a local version RUN touch .Rprofile diff --git a/environment.yml b/environment.yml index 1fde3ddf..2d88b67f 100755 --- a/environment.yml +++ b/environment.yml @@ -1,6 +1,6 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml -name: nf-core-atacseq-1.2.0 +name: nf-core-atacseq-1.2.1 channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 5c08ccbf..29bdf0df 100644 --- a/nextflow.config +++ b/nextflow.config @@ -99,7 +99,7 @@ params { // Container slug. Stable releases should specify release tag! // Developmental code should specify :dev -process.container = 'nfcore/atacseq:1.2.0' +process.container = 'nfcore/atacseq:1.2.1' // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -172,7 +172,7 @@ manifest { description = 'ATACSeq peak-calling and differential analysis pipeline.' mainScript = 'main.nf' nextflowVersion = '>=19.10.0' - version = '1.2.0' + version = '1.2.1' } // Function to ensure that resource requirements don't go beyond From c4b2a9efc7f411d5da61100a863b9c523a06e58e Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 28 Jul 2020 10:39:39 +0200 Subject: [PATCH 2/4] Changelog update --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bf724afa..9afecd1b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [1.2.1] - 2020-07-29 + +* [#118](https://github.com/nf-core/atacseq/issues/118) - Minor patch release to update pipeline schema + ## [1.2.0] - 2020-07-02 ### `Added` From 704acad5d19c9d98d848d774658fd75511647082 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 28 Jul 2020 10:41:31 +0200 Subject: [PATCH 3/4] Update pipeline schema to new format --- nextflow_schema.json | 68 +++++++++++++++++++++++++++++++++++--------- 1 file changed, 55 insertions(+), 13 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 149930a5..d7b3c45c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -4,8 +4,9 @@ "title": "nf-core/atacseq pipeline parameters", "description": "ATACSeq peak-calling and differential analysis pipeline.", "type": "object", - "properties": { - "Input/output options": { + "definitions": { + "input_output_options": { + "title": "Input/output options", "type": "object", "properties": { "input": { @@ -53,7 +54,8 @@ ], "fa_icon": "fas fa-terminal" }, - "Reference genome options": { + "reference_genome_options": { + "title": "Reference genome options", "type": "object", "properties": { "genome": { @@ -136,7 +138,8 @@ }, "fa_icon": "fas fa-dna" }, - "Adapter trimming options": { + "adapter_trimming_options": { + "title": "Adapter trimming options", "type": "object", "properties": { "clip_r1": { @@ -189,7 +192,8 @@ }, "fa_icon": "fas fa-cut" }, - "Alignment options": { + "alignment_options": { + "title": "Alignment options", "type": "object", "properties": { "keep_mito": { @@ -248,7 +252,8 @@ }, "fa_icon": "fas fa-map-signs" }, - "Peak calling options": { + "peak_calling_options": { + "title": "Peak calling options", "type": "object", "properties": { "narrow_peak": { @@ -310,7 +315,8 @@ }, "fa_icon": "fas fa-chart-area" }, - "Differential analysis options": { + "differential_analysis_options": { + "title": "Differential analysis options", "type": "object", "properties": { "deseq2_vst": { @@ -330,7 +336,8 @@ }, "fa_icon": "fas fa-not-equal" }, - "Process skipping options": { + "process_skipping_options": { + "title": "Process skipping options", "type": "object", "properties": { "skip_fastqc": { @@ -384,7 +391,8 @@ }, "fa_icon": "fas fa-forward" }, - "Institutional config options": { + "institutional_config_options": { + "title": "Institutional config options", "type": "object", "properties": { "custom_config_version": { @@ -434,7 +442,8 @@ }, "fa_icon": "fas fa-university" }, - "Max job request options": { + "max_job_request_options": { + "title": "Max job request options", "type": "object", "properties": { "max_cpus": { @@ -464,7 +473,8 @@ }, "fa_icon": "fab fa-acquisitions-incorporated" }, - "Generic options": { + "generic_options": { + "title": "Generic options", "type": "object", "properties": { "help": { @@ -561,5 +571,37 @@ }, "fa_icon": "fas fa-file-import" } - } -} \ No newline at end of file + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/reference_genome_options" + }, + { + "$ref": "#/definitions/adapter_trimming_options" + }, + { + "$ref": "#/definitions/alignment_options" + }, + { + "$ref": "#/definitions/peak_calling_options" + }, + { + "$ref": "#/definitions/differential_analysis_options" + }, + { + "$ref": "#/definitions/process_skipping_options" + }, + { + "$ref": "#/definitions/institutional_config_options" + }, + { + "$ref": "#/definitions/max_job_request_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} From be5cac468a10b99f52c7d980170a414155e27535 Mon Sep 17 00:00:00 2001 From: matthiasho Date: Wed, 29 Jul 2020 12:02:52 +0200 Subject: [PATCH 4/4] =?UTF-8?q?switch=20"skip"=20icon=20to=20=E2=8F=AD?= =?UTF-8?q?=EF=B8=8F?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- nextflow_schema.json | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index d7b3c45c..561b3b7d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -180,7 +180,7 @@ "default": false, "description": "Skip the adapter trimming step.", "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.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "save_trimmed": { "type": "boolean", @@ -224,7 +224,7 @@ "default": false, "description": "Do not perform alignment merging and downstream analysis by merging replicates i.e. only do this by merging resequenced libraries.", "help_text": "An additional series of steps are performed by the pipeline for merging the replicates from the same experimental group. This is primarily to increase the sequencing depth in order to perform downstream analyses such as footprinting. Specifying this parameter means that these steps will not be performed.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "save_align_intermeds": { "type": "boolean", @@ -295,13 +295,13 @@ }, "skip_peak_qc": { "type": "boolean", - "fa_icon": "fas fa-forward", + "fa_icon": "fas fa-fast-forward", "description": "Skip MACS2 peak QC plot generation.", "default": false }, "skip_peak_annotation": { "type": "boolean", - "fa_icon": "fas fa-forward", + "fa_icon": "fas fa-fast-forward", "description": "Skip annotation of MACS2 and consensus peaks with HOMER.", "default": false }, @@ -309,7 +309,7 @@ "type": "boolean", "default": false, "description": "Skip consensus peak generation, annotation and counting.", - "fa_icon": "fas fa-forward", + "fa_icon": "fas fa-fast-forward", "help_text": "" } }, @@ -330,7 +330,7 @@ "type": "boolean", "default": false, "description": "Skip differential accessibility analysis.", - "fa_icon": "fas fa-forward", + "fa_icon": "fas fa-fast-forward", "help_text": "" } }, @@ -344,52 +344,52 @@ "type": "boolean", "default": false, "description": "Skip FastQC.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "skip_picard_metrics": { "type": "boolean", "default": false, "description": "Skip Picard CollectMultipleMetrics.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "skip_preseq": { "type": "boolean", "default": false, "description": "Skip Preseq.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "skip_plot_profile": { "type": "boolean", "default": false, "description": "Skip deepTools plotProfile.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "skip_plot_fingerprint": { "type": "boolean", "default": false, "description": "Skip deepTools plotFingerprint.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "skip_ataqv": { "type": "boolean", "default": false, "description": "Skip Ataqv.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "skip_igv": { "type": "boolean", "default": false, "description": "Skip IGV.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "skip_multiqc": { "type": "boolean", "default": false, "description": "Skip MultiQC.", - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" } }, - "fa_icon": "fas fa-forward" + "fa_icon": "fas fa-fast-forward" }, "institutional_config_options": { "title": "Institutional config options",