step1 nf

scripts/step1.nf

 params.str = 'Hello world!'
 
-params.workingfolder="$(pwd)"
 params.datafolder="/media/superdisk/edna/donnees/rhone_test"
 sequences= Channel.fromFilePairs(params.datafolder+"/*_R{1,2}.fastq.gz",flat:true)
 barcodes=Channel.fromPath(params.datafolder+"/*.dat")
 
+params.count=10
+params.seq_length=20
+params.obiclean_r=0.05
+
 process illuminapairedend {
   """
   [t=2h]paired end alignment then keep reads with quality > 40
   """
   input:
-    set val(id), file(R1_fastq), file(R2_fastq) from sequences
+    set val(run), file(R1_fastq), file(R2_fastq) from sequences
   output:
-    file fastqMerged into fastqMergeds
+    set val(run), file("${run}.merged") into fastqMergeds
   script:
   """
-  illuminapairedend -r $R2_fastq $R1_fastq --score-min=40 > fastqMerged
+  illuminapairedend -r $R2_fastq $R1_fastq --score-min=40 > ${run}.merged
   """
-   }
+}
 
 process remove_unaligned {
   """
   [t=1h]remove unaligned sequence records
   """
   input:
-    file fastqMerged from fastqMergeds
+    set val(run), file("${run}.merged") from fastqMergeds
   output:
-    file mergedAligned into mergedAligneds
+    set val(run), file("${run}.merg.aln") into mergedAligneds
   script:
   """
-  obigrep -p 'mode!="joined"' $fastqMerged > mergedAligned
+  obigrep -p 'mode!="joined"' ${run}.merged > ${run}.merg.aln
   """
 }
                                      
@@ -38,41 +41,87 @@ process assign_sequences {
   [t=6h]assign each sequence record to the corresponding sample/marker combination
   """
   input:
-    file mergedAligned from mergedAligneds
+    set val(run), file("${run}.merg.aln") from mergedAligneds
     file barcode from barcodes
   output:
-    file assignedMerged into assigedMergeds
-    file unassignedMerged into unassignedMergeds
+    set val(run), file("${run}.m.aln.assigned") into assigedMergeds
+    set val(run), file("${run}.m.aln.unassigned") into unassignedMergeds
   script:
   """
-  ngsfilter -t $barcode -u unassignedMerged $mergedAligned --fasta-output > assignedMerged
+  ngsfilter -t $barcode -u ${run}.m.aln.unassigned ${run}.merg.aln --fasta-output > ${run}.m.aln.assigned
   """
 }
 
-
 process split_sequences {
   """
   split the input sequence file in a set of subfiles according to the values of attribute "sample"
   """
   input:
-    file assignedMerged from assigedMergeds
+    set val(run), file("${run}.m.aln.assigned") from assigedMergeds
   output:
-    file 'sample_*.fasta' into demultiplexed mode flatten
+    set val(run), file("sample_${run}_*.fasta") into demultiplexed mode flatten
   script:
   """
-  obisplit -p "sample_" -t sample --fasta $assignedMerged
+  obisplit -p "sample_${run}_" -t sample --fasta ${run}.m.aln.assigned
   """
 }
 
-
 process dereplicate {
+  """
+  dereplicate reads into uniq sequences
+  """
+  input:
+    set val(sample), file("${sample}.fasta") from demultiplexed
+  output:
+    set val(sample), file("${sample}.uniq.fa") into dereplicateds
+  script:
+  """
+  obiuniq -m sample ${sample}.fasta > ${sample}.uniq.fa
+  """
+}
+
+process seq_count_filter {
+  """
+  keep only sequence more than 20bp with no ambiguity IUAPC with total coverage greater than 10 reads
+  """
+  input:
+    set val(sample), file("${sample}.uniq.fa") from dereplicateds
+  output:
+    set val(sample), file("${sample}.u.filtered.fa") into goodlength_goodcounts
+  script:
+  """  
+  obigrep  -p 'count>${params.count}' -s '^[ACGT]+\$' -p 'seq_length>${params.seq_length}' ${sample}.uniq.fa > ${sample}.u.filtered.fa
+  """
+}
+
+
+process annotate_pcrerr {
+  """
+  Clean the sequences for PCR/sequencing errors (sequence variants)
+  """
   input:
-    file sampleSplit from demultiplexed
+    set val(sample), file("${sample}.u.filtered.fa") from goodlength_goodcounts
   output:
-    dereplicated into dereplicateds
+    set val(sample), file("${sample}.u.f.pcr_annotated.fa") into pcrerr_annotateds
   script:
+  if (!file("${sample}.u.filtered.fa").isEmpty()){
   """
-  #dereplicate reads into uniq sequences
-  obiuniq -m sample $sampleSplit > dereplicated
+  obiclean -r ${params.obiclean_r} ${sample}.u.filtered.fa > ${sample}.u.f.pcr_annotated.fa
   """
+  }
 }
+
+process remove_internal {
+  """
+  Remove sequence which are classified as 'internal' by obiclean
+  """
+  input:
+    set val(sample), file("${sample}.u.f.pcr_annotated.fa") from pcrerr_annotateds
+  output:
+    set val(sample), file("${sample}.u.f.p.cleaned.fa") into cleaned_samples
+  script:
+  """
+  obigrep -p 'obiclean_internalcount == 0' ${sample}.u.f.pcr_annotated.fa > ${sample}.u.f.p.cleaned.fa
+  """
+}
+

scripts/step2.nf

+process cat_samples {
+	"""
+	Concatenate sequences from each sample of the same run
+	"""
+	input:
+	  set val(run) from sequences
+	  set val(sample), file("${sample}.u.f.p.cleaned.fa") into cleaned_samples
+	output:
+	  set val(run), file("${run}.fasta") into fastaruns
+	script:
+	"""
+	cat sample_${run}_*.u.f.p.cleaned.fa > ${run}.fasta
+	"""
+}
+WORK IN PROGRESS !
\ No newline at end of file