Merge pull request #171 from nf-core/patch

Update schema to use new definitions groups
nf-core · Jul 29, 2020 · 0f487ed · 0f487ed
2 parents 048fd68 + 2bf81d0
commit 0f487ed
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diff --git 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/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`

diff --git 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
@@ -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
@@ -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

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1,17 +1,18 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$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.",
+    "$schema": "https://json-schema.org/draft-07/schema",
+    "$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.",
     "type": "object",
-    "properties": {
-        "Input/output options": {
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
             "type": "object",
             "properties": {
                 "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": {
@@ -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": {
@@ -165,7 +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",
@@ -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": {
@@ -265,27 +270,28 @@
                 },
                 "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
                 },
                 "skip_consensus_peaks": {
                     "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": ""
                 }
             },
             "fa_icon": "fas fa-chart-area"
         },
-        "Differential analysis options": {
+        "differential_analysis_options": {
+            "title": "Differential analysis options",
             "type": "object",
             "properties": {
                 "deseq2_vst": {
@@ -299,67 +305,69 @@
                     "type": "boolean",
                     "default": false,
                     "description": "Skip differential accessibility analysis.",
-                    "fa_icon": "fas fa-forward",
+                    "fa_icon": "fas fa-fast-forward",
                     "help_text": ""
                 }
             },
             "fa_icon": "fas fa-not-equal"
         },
-        "Process skipping options": {
+        "process_skipping_options": {
+            "title": "Process skipping options",
             "type": "object",
             "properties": {
                 "skip_fastqc": {
                     "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": {
+        "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"
         }
-    }
-}
+    },
+    "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"
+        }
+    ]
+}