Merge pull request #41 from nf-core/dev

Patch Release 1.1.1
nf-core · Jun 23, 2023 · 7451087 · 7451087
2 parents b13f05a + 9ab2141
commit 7451087
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Showing 7 changed files with 74 additions and 8 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -42,3 +42,7 @@ jobs:
       - name: Run pipeline with test data and gene scores
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_scores,docker --outdir ./results
+
+      - name: Run pipeline with test data and duplicate sample ids
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_samples,docker --outdir ./results
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.1 - 2023-06-23
+
+### `Added`
+
+- [#37](https://github.com/nf-core/nanostring/pull/37) - Allow skipping heatmap creation [#38](https://github.com/nf-core/nanostring/issues/38)
+
+### `Fixed`
+
+- [#37](https://github.com/nf-core/nanostring/pull/37) - Use unique rownames for Heatmap creation
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.1.0 - 2023-06-22 - Picometre
 
 ### `Added`

diff --git a/bin/compute_gene_heatmap.R b/bin/compute_gene_heatmap.R
@@ -31,7 +31,7 @@ if (length(args) == 2) {
 counts_selected <- counts %>% dplyr::select(all_of(genes))
 
 #Add proper Rownames
-rownames(counts_selected) <- counts$SAMPLE_ID
+rownames(counts_selected) <- counts$RCC_FILE_NAME
 
 #sort dataframe by rownames to make it easier comparable across heatmaps
 counts_selected[order(row.names(counts_selected)), ]

diff --git a/conf/test_samples.config b/conf/test_samples.config
@@ -0,0 +1,25 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running tests for the same sample with multiple files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/nanostring -profile test_samples,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile with duplicate sample'
+    config_profile_description = 'Test dataset to check pipeline function when we have a duplicate sample id'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test_sampleid.csv'
+
+}
diff --git a/nextflow.config b/nextflow.config
@@ -12,9 +12,13 @@ params {
     // Input options
     input                      = null
 
+    //Skipping options
+    skip_heatmap               = false
+
     // Pipeline options
     heatmap_genes_to_filter    = null
 
+
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes'
@@ -167,9 +171,10 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    test      { includeConfig 'conf/test.config'      }
-    test_full { includeConfig 'conf/test_full.config' }
-    test_scores { includeConfig 'conf/test_scores.config' }
+    test         { includeConfig 'conf/test.config'      }
+    test_full    { includeConfig 'conf/test_full.config' }
+    test_scores  { includeConfig 'conf/test_scores.config' }
+    test_samples { includeConfig 'conf/test_samples.config' }
 }
 
 
@@ -220,7 +225,7 @@ manifest {
     description     = """A Nanostring nCounter analysis pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '1.1.0'
+    version = '1.1.1'
     doi             = ''
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -76,6 +76,18 @@
                 }
             }
         },
+        "skipping_options": {
+            "title": "Skipping Options",
+            "type": "object",
+            "description": "Allows to specify options to skip parts of the pipeline",
+            "default": "",
+            "properties": {
+                "skip_heatmap": {
+                    "type": "boolean",
+                    "description": "Skip creating the heatmap"
+                }
+            }
+        },
         "reference_genome_options": {
             "title": "Reference genome options",
             "type": "object",
@@ -296,6 +308,9 @@
         {
             "$ref": "#/definitions/gene_score_computation"
         },
+        {
+            "$ref": "#/definitions/skipping_options"
+        },
         {
             "$ref": "#/definitions/reference_genome_options"
         },

diff --git a/workflows/nanostring.nf b/workflows/nanostring.nf
@@ -128,10 +128,13 @@ workflow NANOSTRING {
     //
     // MODULE: Compute gene-count heatmap for MultiQC report based on annotated (ENDO) counts
     //
-    CREATE_GENE_HEATMAP (
+    if(!params.skip_heatmap){
+        CREATE_GENE_HEATMAP (
         CREATE_ANNOTATED_TABLES.out.annotated_endo_data
-    )
-    ch_versions = ch_versions.mix(CREATE_GENE_HEATMAP.out.versions)
+        )
+        ch_versions = ch_versions.mix(CREATE_GENE_HEATMAP.out.versions)
+    }
+
 
     //
     // DUMP SOFTWARE VERSIONS