Merge pull request #1 from jpalmer37/allow-per-sample-references

Added compatability for per-sample reference

main.nf

@@ -8,17 +8,42 @@ include { count_variants } from './modules/snippy.nf'
 include { qualimap_bamqc } from './modules/snippy.nf'
 
 workflow {
-  ch_ref = Channel.fromPath( "${params.ref}", type: 'file')
 
+
+
+  // samplesheet input
   if (params.samplesheet_input != 'NO_FILE') {
-    ch_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['R1'], it['R2']] }
+
+    // if --ref file provided, use this reference for all entries
+    if (params.ref != 'NO_FILE'){
+      ch_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['R1'], it['R2']] }
+      ch_ref = ch_fastq.map{it -> it[0]}.combine(Channel.fromPath( "${params.ref}", type: 'file'))
+
+    // if no --ref file provided, look for REF column in the samplesheet on a per-sample basis
+    } else {
+      ch_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['R1'], it['R2'], it['REF']] }
+      ch_ref = ch_fastq.map{it -> [it[0], it[3]]}
+      ch_fastq = ch_fastq.map{it -> it.subList(0,3)}
+    }
+
+  // fastq input 
   } else {
-    ch_fastq = Channel.fromFilePairs( params.fastq_search_path, flat: true ).map{ it -> [it[0].split('_')[0], it[1], it[2]] }.unique{ it -> it[0] }
+    if (params.ref != 'NO_FILE'){
+      ch_fastq = Channel.fromFilePairs( params.fastq_search_path, flat: true ).map{ it -> [it[0].split('_')[0], it[1], it[2]] }.unique{ it -> it[0] }
+      ch_ref = ch_fastq.map{it -> it[0]}.combine(Channel.fromPath( "${params.ref}", type: 'file'))
+    } else {
+      error "ERROR: Reference file must be supplied with --ref when using --fastq_input"
+    }
+
   }
+
+  // FORMAT:
+  // ch_fastq: [sample_id, r1_fastq_path, r2_fastq_path]
+  // ch_ref: [sample_id, reference_path]
 
   main:
     fastp(ch_fastq)
-    snippy(fastp.out.reads.combine(ch_ref))
+    snippy(fastp.out.reads.join(ch_ref))
     qualimap_bamqc(snippy.out.alignment)
-    count_variants(snippy.out.variants_csv.combine(ch_ref))
+    count_variants(snippy.out.variants_csv.join(ch_ref))
 }

nextflow.config

@@ -10,6 +10,7 @@ manifest {
 params {
   samplesheet_input = 'NO_FILE'
   fastq_input = 'NO_FILE'
+  ref = 'NO_FILE'
   illumina_suffixes = ['*_R{1,2}_001', '*_R{1,2}', '*_{1,2}' ]
   fastq_exts = ['.fastq.gz', '.fq.gz', '.fastq', '.fq']
   fastq_search_path = makeFastqSearchPath( illumina_suffixes, fastq_exts )