diff --git a/src/nf_modules/rasusa/main.nf b/src/nf_modules/rasusa/main.nf index e1aefc5803c0ad6c0a37e5f15efbf33796cb7cf1..a76683789494aefe156ae749cee41083c3d23a4b 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 d505124f6533de8cdd7d69b5a8496a96ce047681..261e374bbbcd934c1992f844448884f915bc29ab 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 0000000000000000000000000000000000000000..d66e26f2a334fe43a43b3228b270046d0dbed66c --- /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