From 55235371accd05078a7a776a7b6c2417bac1b5df Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 29 Sep 2021 14:09:47 +0200
Subject: [PATCH] rasusa: add default to no subsampling
---
src/nf_modules/rasusa/main.nf | 15 +++++++++++----
src/nf_modules/rasusa/test.nf | 3 ++-
src/nf_modules/rasusa/test.sh | 4 ++++
3 files changed, 17 insertions(+), 5 deletions(-)
create mode 100644 src/nf_modules/rasusa/test.sh
diff --git a/src/nf_modules/rasusa/main.nf b/src/nf_modules/rasusa/main.nf
index e1aefc58..a7668378 100644
--- a/src/nf_modules/rasusa/main.nf
+++ b/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
}
diff --git a/src/nf_modules/rasusa/test.nf b/src/nf_modules/rasusa/test.nf
index d505124f..261e374b 100644
--- a/src/nf_modules/rasusa/test.nf
+++ b/src/nf_modules/rasusa/test.nf
@@ -1,13 +1,14 @@
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/")
diff --git a/src/nf_modules/rasusa/test.sh b/src/nf_modules/rasusa/test.sh
new file mode 100644
index 00000000..d66e26f2
--- /dev/null
+++ b/src/nf_modules/rasusa/test.sh
@@ -0,0 +1,4 @@
+#! /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"
\ No newline at end of file
--
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