Merge pull request #118 from nf-core/patch

Update schema to use new definitions groups
nf-core · Jul 29, 2020 · 1b3a832 · 1b3a832
2 parents 79bc7c2 + be5cac4
commit 1b3a832
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Showing 6 changed files with 83 additions and 37 deletions.
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/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/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`

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-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
@@ -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
@@ -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

diff --git 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": {
@@ -177,7 +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",
@@ -189,7 +192,8 @@
             },
             "fa_icon": "fas fa-cut"
         },
-        "Alignment options": {
+        "alignment_options": {
+            "title": "Alignment options",
             "type": "object",
             "properties": {
                 "keep_mito": {
@@ -220,7 +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",
@@ -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": {
@@ -290,27 +295,28 @@
                 },
                 "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": {
@@ -324,67 +330,69 @@
                     "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_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": {
+        "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"
         }
-    }
-}
+    },
+    "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"
+        }
+    ]
+}