Add support for samplesheet input

BCCDC-PHL · Oct 12, 2023 · ef52b2c · ef52b2c
1 parent ebc34c2
commit ef52b2c
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Showing 2 changed files with 16 additions and 4 deletions.
diff --git a/conf/illumina.config b/conf/illumina.config
@@ -20,6 +20,10 @@ params {
     fastq_exts = ['.fastq.gz', '.fq.gz']
 
     fastqSearchPath = makeFastqSearchPath( params.illuminaSuffixes, params.fastq_exts )
+
+    // Provide sample ID and fastq paths via a samplesheet.csv with fields:
+    // ID,R1,R2
+    samplesheet_input = 'NO_FILE'
 
     // Use cram input instead of fastq files
     cram = false

diff --git a/main.nf b/main.nf
@@ -22,8 +22,9 @@ if (params.profile){
 }
 
 if ( params.illumina ) {
-   if ( !params.directory ) {
+   if ( !params.directory && params.samplesheet_input == "NO_FILE" ) {
        println("Please supply a directory containing fastqs or CRAMs with --directory. Specify --cram if supplying a CRAMs directory")
+       println("Or provide a samplesheet (headers: ID,R1,R2) with --samplesheet_input")
        println("Use --help to print help")
        System.exit(1)
    }
@@ -78,9 +79,16 @@ workflow {
                   .set{ ch_cramFiles }
        }
        else {
-	   Channel.fromFilePairs( params.fastqSearchPath, flat: true)
-	          .filter{ !( it[0] =~ /Undetermined/ ) }
-	          .set{ ch_filePairs }
+           if ( params.samplesheet_input != "NO_FILE" ) {
+		Channel.fromPath(params.samplesheet_input)
+		    .splitCsv(header: true).map{ it -> [it['ID'], it['R1'], it['R2']] }
+		    .set{ ch_filePairs }
+	    }
+	    else {
+		Channel.fromFilePairs( params.fastqSearchPath, flat: true)
+	            .filter{ !( it[0] =~ /Undetermined/ ) }
+	            .set{ ch_filePairs }
+	    }
        }
    }
    else {