replace bedtools bamtofastq with samtools fastq (direct fastq.gz)

modules/prokka.nf

@@ -13,12 +13,7 @@ process PROKKA {
   """
   prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus}
   rm PROKKA_${sampleId}/*.gbk
-
-  gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt
-  if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt
-  then
-    rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt 
-  fi
+  gt gff3validator PROKKA_${sampleId}/${sampleId}.gff 
   """
 }
 

modules/reads_deduplication.nf

@@ -24,8 +24,7 @@ process READS_DEDUPLICATION {
   samtools idxstats ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.idxstats
   samtools flagstat ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.flagstat
   samtools sort -n -o ${sampleId}.filtered.sort.bam ${sampleId}.filtered.bam
-  bedtools bamtofastq -i ${sampleId}.filtered.sort.bam -fq ${sampleId}_R1_dedup.fastq -fq2 ${sampleId}_R2_dedup.fastq
-  gzip ${sampleId}_R1_dedup.fastq ; gzip ${sampleId}_R2_dedup.fastq
+  samtools fastq -N -1 ${sampleId}_R1_dedup.fastq.gz -2 ${sampleId}_R2_dedup.fastq.gz ${sampleId}.filtered.sort.bam 
   rm ${sampleId}.sort.bam
   rm ${sampleId}.fixmate.bam
   rm ${sampleId}.fixmate.positionsort.bam