From b74bc6428c2e3a53f1ab5f09be3200578987d7fb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 25 Jul 2018 17:48:29 +0200
Subject: [PATCH] Cleanup SRAtoolkit files
---
README.md | 4 +--
src/nf_modules/SRAtoolkit/sratoolkit.config | 25 ++++++++++++++++
.../sra-tools.nf => SRAtoolkit/sratoolkit.nf} | 28 +++++++++---------
.../tests/fastqdump.nf | 29 ++++++++++---------
.../tests/list-srr.txt | 0
src/nf_modules/SRAtoolkit/tests/tests.sh | 4 +++
src/nf_modules/sra-tools/sra-tools.config | 17 -----------
src/nf_modules/sra-tools/tests/tests.sh | 4 ---
8 files changed, 59 insertions(+), 52 deletions(-)
create mode 100644 src/nf_modules/SRAtoolkit/sratoolkit.config
rename src/nf_modules/{sra-tools/sra-tools.nf => SRAtoolkit/sratoolkit.nf} (68%)
rename src/nf_modules/{sra-tools => SRAtoolkit}/tests/fastqdump.nf (60%)
rename src/nf_modules/{sra-tools => SRAtoolkit}/tests/list-srr.txt (100%)
create mode 100755 src/nf_modules/SRAtoolkit/tests/tests.sh
delete mode 100644 src/nf_modules/sra-tools/sra-tools.config
delete mode 100755 src/nf_modules/sra-tools/tests/tests.sh
diff --git a/README.md b/README.md
index 9429d2d..1c35270 100644
--- a/README.md
+++ b/README.md
@@ -89,7 +89,7 @@ Kallisto | ok | ok | ok
MultiQC | ok | ok | ok
RSEM | ok | ok | ok
SAMtools | ok | ok | ok
-SRAtoolkit | **no** | ok | ok
+SRAtoolkit | ok | ok | ok
Salmon | **no** | ok | ok
TopHat | **no** | ok | ok
Trimmomatic | **no** | ok | ok
@@ -99,8 +99,6 @@ cutadapt | ok | ok | ok
deepTools | **no** | ok | ok
file_handle | **no** | ok | ok
pigz | **no** | ok | ok
-sra-tools | ok | **no** | **no**
-
## Contributing
diff --git a/src/nf_modules/SRAtoolkit/sratoolkit.config b/src/nf_modules/SRAtoolkit/sratoolkit.config
new file mode 100644
index 0000000..128a4fe
--- /dev/null
+++ b/src/nf_modules/SRAtoolkit/sratoolkit.config
@@ -0,0 +1,25 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $fastq_dump {
+ container = "sratoolkit:2.8.2"
+ }
+ }
+ }
+ sge {
+ process{
+ $fastq_dump {
+ beforeScript = "module purge; module load SRAtoolkit/2.8.2"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/sra-tools/sra-tools.nf b/src/nf_modules/SRAtoolkit/sratoolkit.nf
similarity index 68%
rename from src/nf_modules/sra-tools/sra-tools.nf
rename to src/nf_modules/SRAtoolkit/sratoolkit.nf
index 0ffa4f3..9fce5e4 100644
--- a/src/nf_modules/sra-tools/sra-tools.nf
+++ b/src/nf_modules/SRAtoolkit/sratoolkit.nf
@@ -20,24 +20,24 @@ Channel
//run is the column name containing SRR ids
- process fastq-dump {
+process fastq_dump {
tag {"${x.run}"}
publishDir "results/download/fastq/${x.run}/", mode: 'copy'
+
input:
- val x from SRR
+ val x from SRR
+
output:
- file("*") into fastq
+ file("*") into fastq
script:
-
- """
-
- fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" ${x.run}
- if [ -f ${x.run}_1.fastq ]
- then
- true
- else
- touch ${x.run}.fastq
- fi
"""
- }
+fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" ${x.run}
+if [ -f ${x.run}_1.fastq ]
+then
+ true
+else
+ touch ${x.run}.fastq
+fi
+"""
+}
diff --git a/src/nf_modules/sra-tools/tests/fastqdump.nf b/src/nf_modules/SRAtoolkit/tests/fastqdump.nf
similarity index 60%
rename from src/nf_modules/sra-tools/tests/fastqdump.nf
rename to src/nf_modules/SRAtoolkit/tests/fastqdump.nf
index 8fdd50e..32579e7 100644
--- a/src/nf_modules/sra-tools/tests/fastqdump.nf
+++ b/src/nf_modules/SRAtoolkit/tests/fastqdump.nf
@@ -20,24 +20,25 @@ Channel
//run is the column name containing SRR ids
- process fastqdump {
+process fastq_dump {
tag {"${x.run}"}
publishDir "results/download/fastq/${x.run}/", mode: 'copy'
+
input:
- val x from SRR
+ val x from SRR
+
output:
- file("*") into fastq
+ file("*") into fastq
script:
-
- """
- #for test only 10000 reads are downloading with the option -N 10000 -X 20000
- fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${x.run}
- if [ -f ${x.run}_1.fastq ]
- then
- true
- else
- touch ${x.run}.fastq
- fi
"""
- }
+#for test only 10000 reads are downloading with the option -N 10000 -X 20000
+fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${x.run}
+if [ -f ${x.run}_1.fastq ]
+then
+ true
+else
+ touch ${x.run}.fastq
+fi
+"""
+}
diff --git a/src/nf_modules/sra-tools/tests/list-srr.txt b/src/nf_modules/SRAtoolkit/tests/list-srr.txt
similarity index 100%
rename from src/nf_modules/sra-tools/tests/list-srr.txt
rename to src/nf_modules/SRAtoolkit/tests/list-srr.txt
diff --git a/src/nf_modules/SRAtoolkit/tests/tests.sh b/src/nf_modules/SRAtoolkit/tests/tests.sh
new file mode 100755
index 0000000..c5efbcc
--- /dev/null
+++ b/src/nf_modules/SRAtoolkit/tests/tests.sh
@@ -0,0 +1,4 @@
+nextflow src/nf_modules/SRAtoolkit/tests/fastqdump.nf \
+ -c src/nf_modules/SRAtoolkit/sratoolkit.config \
+ -profile docker \
+ --list_srr "src/nf_modules/SRAtoolkit/tests/list-srr.txt"
diff --git a/src/nf_modules/sra-tools/sra-tools.config b/src/nf_modules/sra-tools/sra-tools.config
deleted file mode 100644
index c49af21..0000000
--- a/src/nf_modules/sra-tools/sra-tools.config
+++ /dev/null
@@ -1,17 +0,0 @@
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $fastqdump {
- container = "sratoolkit:2.8.2"
- } }
- }
- sge {
- process{
- $fastqdump {
- beforeScript = "module purge; module load SRAtoolkit/2.8.2"
- }
- }
- }
-}
diff --git a/src/nf_modules/sra-tools/tests/tests.sh b/src/nf_modules/sra-tools/tests/tests.sh
deleted file mode 100755
index 59e6c55..0000000
--- a/src/nf_modules/sra-tools/tests/tests.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-nextflow src/nf_modules/sra-tools/tests/fastqdump.nf \
- -c src/nf_modules/sra-tools/sra-tools.config \
- -profile docker \
- --list_srr "src/nf_modules/sra-tools/tests/list-srr.txt"
--
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