rasusa: add default to no subsampling

src/nf_modules/rasusa/main.nf

@@ -4,7 +4,7 @@ container_url = "lbmc/rasusa:${version}"
 include { index_fasta } from "./../samtools/main.nf"
 
 params.sample_fastq = ""
-params.sample_fastq_coverage = "1.0"
+params.sample_fastq_coverage = ""
 params.sample_fastq_size = ""
 params.sample_fastq_out = ""
 workflow sample_fastq {
@@ -13,11 +13,18 @@ workflow sample_fastq {
   fasta
 
   main:
-  index_fasta(fasta)
-  sub_sample_fastq(fastq, index_fasta.out.index)
+  if (params.sample_fastq_coverage == "" && params.sample_fastq_size == ""){
+    fastq
+      .set{ final_fastq }
+  } else {
+    index_fasta(fasta)
+    sub_sample_fastq(fastq, index_fasta.out.index)
+    sub_sample_fastq.out.fastq
+      .set{ final_fastq }
+  }
 
   emit:
-  fastq = sub_sample_fastq.out.fastq
+  fastq = final_fastq
 
 }
 

src/nf_modules/rasusa/test.nf

 nextflow.enable.dsl=2
 
 /*
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq"
 ./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" --coverage 1.0
 ./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq" --size "1Mb"
 */
 
 params.fastq = "data/fastq/*R{1,2}*"
 params.fasta = "data/fasta/*.fasta"
-params.coverage = "2.0"
+params.coverage = ""
 params.size = ""
 
 include { sample_fastq } from "./main.nf" addParams(sample_fastq_coverage: params.coverage, sample_fastq_size: params.size, sample_fastq_out: "sample/")

src/nf_modules/rasusa/test.sh

+#! /bin/sh
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq"
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" --coverage 1.0
+./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq" --size "1Mb"
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