implement suggested changes & add params to schema

nf-core · Oct 31, 2024 · 82d97d2 · 82d97d2
1 parent 34dc6e5
commit 82d97d2
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Showing 6 changed files with 71 additions and 9 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,7 +33,7 @@
 - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237))
 - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
-- init ([#3261](https://github.com/nf-core/tools/pull/3261))
+- Add `downstream_samplesheets` to skip_features and GENERATE_DOWNSTREAM_SAMPLESHEETS to template ([#3261](https://github.com/nf-core/tools/pull/3261))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
@@ -32,9 +32,9 @@ params {
     genome = 'R64-1-1'
     {%- endif %}
 
-    {% if downstream_samplesheets -%}
+    {% if downstream_samplesheet -%}
     // Downstream samplesheets
     generate_downstream_samplesheets = true
-    generate_pipeline_samplesheets   = 'rnaseq'
+    generate_pipeline_samplesheets   = 'rnaseq,sarek'
     {%- endif %}
 }
diff --git a/nf_core/pipeline-template/conf/test_full.config b/nf_core/pipeline-template/conf/test_full.config
@@ -27,9 +27,9 @@ params {
     fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
     {%- endif %}
 
-    {% if downstream_samplesheets -%}
+    {% if downstream_samplesheet -%}
     // Downstream samplesheets
     generate_downstream_samplesheets = true
-    generate_pipeline_samplesheets   = 'rnaseq'
+    generate_pipeline_samplesheets   = 'sarek,rnaseq'
     {%- endif %}
 }
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
@@ -86,6 +86,30 @@
             }
         },
         {%- endif %}
+        {% if downstream_samplesheet %}
+        "generate_samplesheet_options": {
+            "title": "Downstream pipeline samplesheet generation options",
+            "type": "object",
+            "fa_icon": "fas fa-university",
+            "description": "Options for generating input samplesheets for complementary downstream pipelines.",
+            "properties": {
+                "generate_downstream_samplesheets": {
+                    "type": "boolean",
+                    "description": "Turn on generation of samplesheets for downstream pipelines."
+                },
+                "generate_pipeline_samplesheets": {
+                    "type": "string",
+                    "description": "Specify a comma separated string in quotes to specify which pipeline to generate a samplesheet for.",
+                    "pattern": "^(rnaseq|sarek)(?:,(sarek|rnaseq)){0,1}"
+                },
+                "generate_pipeline_samplesheets_format": {
+                    "type": "string",
+                    "description": "Specify the output format of the samplesheet.",
+                    "enum": ["txt", "tsv", "csv"],
+                }
+            }
+        },
+        {%- endif %}
         {%- if nf_core_configs %}
         "institutional_config_options": {
             "title": "Institutional config options",

diff --git a/nf_core/pipeline-template/subworkflows/local/generate_downstream_samplesheets/main.nf b/nf_core/pipeline-template/subworkflows/local/generate_downstream_samplesheets/main.nf
@@ -7,15 +7,17 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO: Update the following workflow to a specific pipeline
+// TODO nf-core: Update the following workflow to a specific pipeline
 workflow SAMPLESHEET_RNASEQ {
     take:
     ch_reads
     format
 
     main:
 
+    //TODO nf-core: customise to your needs
     ch_list_for_samplesheet = ch_reads.map { meta, reads ->
+        //TODO nf-core: Update the path to the published output directory of the reads
         def out_path     = file(params.outdir).toString() + '/relative/custom/path/'
         def sample       = meta.id
         def fastq_1      = meta.single_end  ? out_path + reads.getName() : out_path + reads[0].getName()
@@ -27,6 +29,35 @@ workflow SAMPLESHEET_RNASEQ {
     channelToSamplesheet(ch_list_for_samplesheet, "${params.outdir}/downstream_samplesheets/rnaseq", format)
 }
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    SUBWORKFLOW SPECIFIC FOR SAREK
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+// TODO nf-core: Update the following workflow to a specific pipeline
+workflow SAMPLESHEET_SAREK {
+    take:
+    ch_reads
+    format
+
+    main:
+
+    //TODO nf-core: customise to your needs
+    ch_list_for_samplesheet = ch_reads.map { meta, reads ->
+        //TODO nf-core: Update the path to the published output directory of the reads
+        def out_path     = file(params.outdir).toString() + '/relative/custom/path/'
+        def patient      = meta.id
+        def sample       = meta.id
+        def lane         = ""
+        def fastq_1      = meta.single_end  ? out_path + reads.getName() : out_path + reads[0].getName()
+        def fastq_2      = !meta.single_end ? out_path + reads[1].getName() : ""
+        [ patient: patient, sample: sample, lane: lane, fastq_1: fastq_1, fastq_2: fastq_2 ]
+    }
+
+    channelToSamplesheet(ch_list_for_samplesheet, "${params.outdir}/downstream_samplesheets/rnaseq", format)
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW CALLING PIPELINE SPECIFIC SAMPLESHEET GENERATION
@@ -40,13 +71,20 @@ workflow GENERATE_DOWNSTREAM_SAMPLESHEETS {
     main:
     def downstreampipeline_names = params.generate_pipeline_samplesheets.split(",")
 
-    // TODO: Add more pipelines here
+    // TODO nf-coee: Add more pipelines here
     if (downstreampipeline_names.contains('rnaseq')) {
         SAMPLESHEET_RNASEQ(
             input,
             params.generate_pipeline_samplesheets_format
         )
     }
+
+    if (downstreampipeline_names.contains('rnaseq')) {
+        SAMPLESHEET_SAREK(
+            input,
+            params.generate_pipeline_samplesheets_format
+        )
+    }
 }
 
 // Input can be any channel with a dictionary

diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
@@ -285,9 +285,9 @@ downstream_samplesheet:
   short_description: "Generate downstream samplesheets"
   description: "The pipeline will include the generate_downstream_samplesheets subworkflow for the generation of a samplesheet for other downstream pipelines."
   help_text: |
-    The pipeline will include the generate_downstream_samplesheets subworkflow.
+    The pipeline will include the `GENERATE_DOWNSTREAM_SAMPLESHEETS` subworkflow.
 
-    The subworkflow generate_downstream_samplesheets provides a base template for generating samplesheets by taking a specified input channel of i.e. reads or fasta extracts its metadata for generating samplesheets.
+    The subworkflow `GENERATE_DOWNSTREAM_SAMPLESHEETS` provides a base template for generating samplesheets by taking a specified input channel of reads or fasta and extracts its metadata for generating samplesheets.
   nfcore_pipelines: True
   custom_pipelines: True
 changelog: