refactor: Use fromSamplesheet instead of input_check

nf-core · Aug 25, 2023 · 7910cc1 · 7910cc1
1 parent 16007cf
commit 7910cc1
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Showing 4 changed files with 25 additions and 98 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -10,7 +10,8 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"]
             },
             "fastq_1": {
                 "type": "string",

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
diff --git a/workflows/methylseq.nf b/workflows/methylseq.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
 
 def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
 def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
@@ -35,7 +35,6 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
 //
 // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules
 //
-include { INPUT_CHECK } from '../subworkflows/local/input_check'
 include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
 
 // Aligner: bismark or bismark_hisat
@@ -84,31 +83,34 @@ workflow METHYLSEQ {
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     //
-    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    // Create input channel from input file provided through params.input
     //
-    INPUT_CHECK (
-        file(params.input)
-    )
-    .reads
-    .map {
-        meta, fastq ->
+    Channel
+        .fromSamplesheet("input")
+        .map {
+            meta, fastq_1, fastq_2 ->
+            if (!fastq_2) {
+                return [ meta + [ single_end:true ], [ fastq_1 ] ]
+            } else {
+                return [ meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
+            }
+        }
+        .groupTuple()
+        .map {
+            meta, fastq ->
             def meta_clone = meta.clone()
             meta_clone.id = meta_clone.id.split('_')[0..-2].join('_')
             [ meta_clone, fastq ]
-    }
-    .groupTuple(by: [0])
-    .branch {
-        meta, fastq ->
+        }
+        .groupTuple(by: [0])
+        .branch {
+            meta, fastq ->
             single: fastq.size() == 1
-                return [ meta, fastq.flatten() ]
+            return [ meta, fastq.flatten() ]
             multiple: fastq.size() > 1
-                return [ meta, fastq.flatten() ]
-    }
-    .set { ch_fastq }
-    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
-    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
-    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
-    // ! There is currently no tooling to help you write a sample sheet schema
+            return [ meta, fastq.flatten() ]
+        }
+        .set { ch_fastq }
 
     //
     // MODULE: Concatenate FastQ files from same sample if required