SRAtoolkit: update nf strcuture and improve script

src/nf_modules/SRAtoolkit/tests/fastqdump.nf → src/nf_modules/SRAtoolkit/fastqdump.nf

@@ -15,30 +15,33 @@ log.info "downloading list srr : ${params.list_srr}"
 Channel
   .fromPath( params.list_srr )
   .ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" }
-  .splitCsv(header: true)
+  .splitCsv()
+  .map { it -> it[0]}
   .set { SRR }
 
 //run is the column name containing SRR ids
 
 process fastq_dump {
-  tag {"${x.run}"}
-  publishDir "results/download/fastq/${x.run}/", mode: 'copy'
+  tag "$file_id"
+  publishDir "results/download/fastq/${file_id}/", mode: 'copy'
 
   input:
-    val x  from SRR
+    val file_id from SRR
 
   output:
-    file("*") into fastq
+    set file_id, "*.fastq" 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 ]
+fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${file_id}
+if [ -f ${file_id}_1.fastq ]
 then
-  true
-else
-  touch ${x.run}.fastq
+  mv ${file_id}_1.fastq ${file_id}_R1.fastq
+fi
+if [ -f ${file_id}_2.fastq ]
+then
+  mv ${file_id}_2.fastq ${file_id}_R2.fastq
 fi
 """
 }

src/nf_modules/SRAtoolkit/tests/list-srr.txt → src/nf_modules/SRAtoolkit/list-srr.txt

-run
 ERR572281
 ERR572146
 ERR572201

src/nf_modules/SRAtoolkit/sratoolkit.nf

-/*
-* sra-tools :
-
-*/
-
-/*                      fastq-dump
-* Imputs : srr list
-* Outputs : fastq files
-*/
-
-params.list_srr = "$baseDir/data/SRR/*.txt"
-
-log.info "downloading list srr : ${params.list_srr}"
-
-Channel
-  .fromPath( params.list_srr )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" }
-  .splitCsv(header: true)
-  .set { SRR }
-
-//run is the column name containing SRR ids
-
-process fastq_dump {
-  tag {"${x.run}"}
-  publishDir "results/download/fastq/${x.run}/", mode: 'copy'
-
-  input:
-    val x  from SRR
-
-  output:
-    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
-"""
-}

src/nf_modules/SRAtoolkit/tests.sh

+nextflow src/nf_modules/SRAtoolkit/fastqdump.nf \
+  -c src/nf_modules/SRAtoolkit/fastqdump.config \
+  -profile docker \
+  --list_srr "src/nf_modules/SRAtoolkit/list-srr.txt"

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"