Cleanup SRAtoolkit files

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

src/nf_modules/sra-tools/sra-tools.config → src/nf_modules/SRAtoolkit/sratoolkit.config

@@ -3,14 +3,22 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $fastqdump {
-      container = "sratoolkit:2.8.2"
-      }    }
+      $fastq_dump {
+        container = "sratoolkit:2.8.2"
+      }
+    }
   }
   sge {
     process{
-      $fastqdump {
+      $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'
       }
     }
   }

src/nf_modules/sra-tools/sra-tools.nf → 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
+"""
+}

src/nf_modules/sra-tools/tests/fastqdump.nf → 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
+"""
+}

src/nf_modules/SRAtoolkit/tests/tests.sh

+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"

src/nf_modules/sra-tools/tests/tests.sh

-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"