From 2a991dc630a3f180d4745772bb55b13280916802 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 14:19:57 +0200
Subject: [PATCH] BEDtools: update nf structure
---
...{bedtools.config => fasta_from_bed.config} | 0
.../{bedtools.nf => fasta_from_bed.nf} | 0
src/nf_modules/BEDtools/{tests => }/tests.sh | 4 +--
.../BEDtools/tests/fasta_from_bed.nf | 33 -------------------
4 files changed, 2 insertions(+), 35 deletions(-)
rename src/nf_modules/BEDtools/{bedtools.config => fasta_from_bed.config} (100%)
rename src/nf_modules/BEDtools/{bedtools.nf => fasta_from_bed.nf} (100%)
rename src/nf_modules/BEDtools/{tests => }/tests.sh (52%)
delete mode 100644 src/nf_modules/BEDtools/tests/fasta_from_bed.nf
diff --git a/src/nf_modules/BEDtools/bedtools.config b/src/nf_modules/BEDtools/fasta_from_bed.config
similarity index 100%
rename from src/nf_modules/BEDtools/bedtools.config
rename to src/nf_modules/BEDtools/fasta_from_bed.config
diff --git a/src/nf_modules/BEDtools/bedtools.nf b/src/nf_modules/BEDtools/fasta_from_bed.nf
similarity index 100%
rename from src/nf_modules/BEDtools/bedtools.nf
rename to src/nf_modules/BEDtools/fasta_from_bed.nf
diff --git a/src/nf_modules/BEDtools/tests/tests.sh b/src/nf_modules/BEDtools/tests.sh
similarity index 52%
rename from src/nf_modules/BEDtools/tests/tests.sh
rename to src/nf_modules/BEDtools/tests.sh
index f27c274..4d6bda0 100755
--- a/src/nf_modules/BEDtools/tests/tests.sh
+++ b/src/nf_modules/BEDtools/tests.sh
@@ -1,5 +1,5 @@
-nextflow src/nf_modules/BEDtools/tests/fasta_from_bed.nf \
- -c src/nf_modules/BEDtools/bedtools.config \
+nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
+ -c src/nf_modules/BEDtools/fasta_from_bed.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--bed "data/tiny_dataset/annot/tiny.bed" \
diff --git a/src/nf_modules/BEDtools/tests/fasta_from_bed.nf b/src/nf_modules/BEDtools/tests/fasta_from_bed.nf
deleted file mode 100644
index 372f89e..0000000
--- a/src/nf_modules/BEDtools/tests/fasta_from_bed.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-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
-"""
-}
--
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