From b6575e6531cfac4426b585d52c18eb76cc2d9340 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Jun 2018 09:54:17 +0200
Subject: [PATCH] BEDtools: add tests files
---
src/nf_modules/BEDtools/bedtools.nf | 4 +--
.../BEDtools/tests/fasta_from_bed.nf | 33 +++++++++++++++++++
src/nf_modules/BEDtools/tests/tests.sh | 5 +++
3 files changed, 40 insertions(+), 2 deletions(-)
create mode 100644 src/nf_modules/BEDtools/tests/fasta_from_bed.nf
create mode 100755 src/nf_modules/BEDtools/tests/tests.sh
diff --git a/src/nf_modules/BEDtools/bedtools.nf b/src/nf_modules/BEDtools/bedtools.nf
index 09ab4af..5c85aa6 100644
--- a/src/nf_modules/BEDtools/bedtools.nf
+++ b/src/nf_modules/BEDtools/bedtools.nf
@@ -21,7 +21,7 @@ Channel
.set { bed_files }
process fasta_from_bed {
- tag "$pair_id"
+ tag "${bed.baseName}"
cpus 4
publishDir "results/fasta/", mode: 'copy'
@@ -35,6 +35,6 @@ process fasta_from_bed {
script:
"""
bedtools getfasta -name \
--fi ${fasta} -bed ${bed} -fo ${fasta.baseName}_extracted.fasta
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
"""
}
diff --git a/src/nf_modules/BEDtools/tests/fasta_from_bed.nf b/src/nf_modules/BEDtools/tests/fasta_from_bed.nf
new file mode 100644
index 0000000..372f89e
--- /dev/null
+++ b/src/nf_modules/BEDtools/tests/fasta_from_bed.nf
@@ -0,0 +1,33 @@
+params.fastq = "$baseDir/data/fasta/*.fasta"
+params.bed = "$baseDir/data/annot/*.bed"
+
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
+
+Channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .set { fasta_files }
+Channel
+ .fromPath( params.bed )
+ .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+ .set { bed_files }
+
+process fasta_from_bed {
+ tag "${bed.baseName}"
+ cpus 4
+ publishDir "results/fasta/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files
+ file bed from bed_files
+
+ output:
+ file "*_extracted.fasta" into fasta_files_extracted
+
+ script:
+"""
+bedtools getfasta -name \
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
+"""
+}
diff --git a/src/nf_modules/BEDtools/tests/tests.sh b/src/nf_modules/BEDtools/tests/tests.sh
new file mode 100755
index 0000000..f27c274
--- /dev/null
+++ b/src/nf_modules/BEDtools/tests/tests.sh
@@ -0,0 +1,5 @@
+nextflow src/nf_modules/BEDtools/tests/fasta_from_bed.nf \
+ -c src/nf_modules/BEDtools/bedtools.config \
+ -profile docker \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ --bed "data/tiny_dataset/annot/tiny.bed" \
--
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