From 84d09c3f63122d42a9e2bcb65954cc663e44130c Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 28 Jul 2020 10:27:22 +0200 Subject: [PATCH 1/6] Update schema to use new definitions groups --- nextflow_schema.json | 68 +++++++++++++++++++++++++++++++++++--------- 1 file changed, 55 insertions(+), 13 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5614b18c1..2c98a1e38 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": { @@ -124,7 +126,8 @@ }, "fa_icon": "fas fa-dna" }, - "Adapter trimming options": { + "adapter_trimming_options": { + "title": "Adapter trimming options", "type": "object", "properties": { "clip_r1": { @@ -177,7 +180,8 @@ }, "fa_icon": "fas fa-cut" }, - "Alignment options": { + "alignment_options": { + "title": "Alignment options", "type": "object", "properties": { "keep_dups": { @@ -223,7 +227,8 @@ }, "fa_icon": "fas fa-map-signs" }, - "Peak calling options": { + "peak_calling_options": { + "title": "Peak calling options", "type": "object", "properties": { "narrow_peak": { @@ -285,7 +290,8 @@ }, "fa_icon": "fas fa-chart-area" }, - "Differential analysis options": { + "differential_analysis_options": { + "title": "Differential analysis options", "type": "object", "properties": { "deseq2_vst": { @@ -305,7 +311,8 @@ }, "fa_icon": "fas fa-not-equal" }, - "Process skipping options": { + "process_skipping_options": { + "title": "Process skipping options", "type": "object", "properties": { "skip_fastqc": { @@ -359,7 +366,8 @@ }, "fa_icon": "fas fa-forward" }, - "Institutional config options": { + "institutional_config_options": { + "title": "Institutional config options", "type": "object", "properties": { "custom_config_version": { @@ -409,7 +417,8 @@ }, "fa_icon": "fas fa-university" }, - "Max job request options": { + "max_job_request_options": { + "title": "Max job request options", "type": "object", "properties": { "max_cpus": { @@ -439,7 +448,8 @@ }, "fa_icon": "fab fa-acquisitions-incorporated" }, - "Generic options": { + "generic_options": { + "title": "Generic options", "type": "object", "properties": { "help": { @@ -536,5 +546,37 @@ }, "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 e240613c256defa3697e6229b8710b5921ce84a2 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 28 Jul 2020 10:31:52 +0200 Subject: [PATCH 2/6] 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 6c65240bd..5740990aa 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/chipseq:1.2.0 + run: docker build --no-cache . -t nfcore/chipseq:1.2.1 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/chipseq:dev - docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0 + docker tag nfcore/chipseq:dev nfcore/chipseq: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/chipseq:1.2.0 + run: docker build --no-cache . -t nfcore/chipseq:1.2.1 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/chipseq:dev - docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0 + docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.1 - name: Install Nextflow run: | diff --git a/Dockerfile b/Dockerfile index 0628abe4a..44ec4adfa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,10 +7,10 @@ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-chipseq-1.2.0/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-chipseq-1.2.1/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-chipseq-1.2.0 > nf-core-chipseq-1.2.0.yml +RUN conda env export --name nf-core-chipseq-1.2.1 > nf-core-chipseq-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 112077221..67a21782d 100644 --- 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-chipseq-1.2.0 +name: nf-core-chipseq-1.2.1 channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 4e54affdf..561fe9d7a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -96,7 +96,7 @@ params { // Container slug. Stable releases should specify release tag! // Developmental code should specify :dev -process.container = 'nfcore/chipseq:1.2.0' +process.container = 'nfcore/chipseq:1.2.1' // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -169,7 +169,7 @@ manifest { description = 'ChIP-seq 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 d42c010bde7a098dc3941c1db013d0a22d976644 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 28 Jul 2020 10:35:45 +0200 Subject: [PATCH 3/6] Update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aafc386f0..fc587ef09 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 + +* [#171](https://github.com/nf-core/chipseq/issues/171) - Minor patch release to update pipeline schema + ## [1.2.0] - 2020-07-02 ### `Added` From 7827e471d0f35b4e23214869486ea8fb9280a457 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 28 Jul 2020 10:44:13 +0200 Subject: [PATCH 4/6] Fix atacseq copy-paste errors --- nextflow_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 2c98a1e38..d091e787f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,8 +1,8 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/nf-core/atacseq/master/nextflow_schema.json", - "title": "nf-core/atacseq pipeline parameters", - "description": "ATACSeq peak-calling and differential analysis pipeline.", + "$id": "https://raw.githubusercontent.com/nf-core/chipseq/master/nextflow_schema.json", + "title": "nf-core/chipseq pipeline parameters", + "description": "ChIP-seq peak-calling and differential analysis pipeline.", "type": "object", "definitions": { "input_output_options": { @@ -12,7 +12,7 @@ "input": { "type": "string", "description": "Path to comma-separated file containing information about the samples in the experiment.", - "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).", + "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).", "fa_icon": "fas fa-file-csv" }, "single_end": { From e7173bde5de9b447abe7842f37a5e3a233a7a975 Mon Sep 17 00:00:00 2001 From: matthiasho Date: Wed, 29 Jul 2020 11:58:09 +0200 Subject: [PATCH 5/6] =?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 d091e787f..27e0bfbfe 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -168,7 +168,7 @@ "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", @@ -270,13 +270,13 @@ }, "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 }, @@ -284,7 +284,7 @@ "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": "" } }, @@ -305,7 +305,7 @@ "type": "boolean", "default": false, "description": "Skip differential accessibility analysis.", - "fa_icon": "fas fa-forward", + "fa_icon": "fas fa-fast-forward", "help_text": "" } }, @@ -319,52 +319,52 @@ "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_spp": { "type": "boolean", "default": false, "description": "Skip Phantompeakqualtools.", - "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", @@ -579,4 +579,4 @@ "$ref": "#/definitions/generic_options" } ] -} +} \ No newline at end of file From 2bf81d055ab795eb53f7bace396c55367238201c Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 29 Jul 2020 17:55:56 +0200 Subject: [PATCH 6/6] https for schema URL --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 27e0bfbfe..8409c9d85 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/chipseq/master/nextflow_schema.json", "title": "nf-core/chipseq pipeline parameters", "description": "ChIP-seq peak-calling and differential analysis pipeline.", @@ -579,4 +579,4 @@ "$ref": "#/definitions/generic_options" } ] -} \ No newline at end of file +}