Prepared version to Alia to Test and Training.

.gitignore

 .nextflow*
-.Rhistory
+.Rhistory
\ No newline at end of file
+work/
+work/*
+bin/*
+results/*
\ No newline at end of file

src/bolero.nf

@@ -159,17 +159,18 @@ if(!params.skipBC) {
 }
 
 // Replace concatenate by seqkit fct to parallelization:
-include { concatenate } from "./nf_modules/concatenate/main.nf"
 // include { concatenate } from "./nf_modules/seqkit/main.nf"
+include { concatenate } from "./nf_modules/concatenate/main.nf"
+
 include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
 include { hbv_genome } from "./nf_modules/minimap2/main.nf"
 include { seqkit_grep } from "./nf_modules/seqkit/main.nf"
-include { sort_bam as sort_bam_genome } from './nf_modules/samtools/main.nf' addParams(sort_bam_out: 'minimap2_genome')
-include { index_bam as index_bam_genome } from './nf_modules/samtools/main.nf' addParams(index_bam_out: 'minimap2_genome')
+include { sort_bam as sort_bam_genome } from './nf_modules/samtools/main.nf' addParams(sort_bam_out: params.minimap2_genome_out)
+include { index_bam as index_bam_genome } from './nf_modules/samtools/main.nf' addParams(index_bam_out: params.minimap2_genome_out)
 include { start_position_counts } from "./nf_modules/samtools/main.nf"
 
 // creation des fonctions NanoSplicer:
-include { jwr_check } from "./nf_modules/nanosplicer/main.nf"
+// include { jwr_check } from "./nf_modules/nanosplicer/main.nf"
 
 /*
  ****************************************************************
@@ -198,8 +199,9 @@ workflow {
     }
   }
   //####################### PREPROCESSING #######################
-  
-  seqkit_grep(porechop.out.porechoped_fastq, params.adapt, params.gsp)
+
+  /*
+  seqkit_grep(concatenate.out.merged_fastq, params.adapt, params.gsp)
   cut_5pRACE(seqkit_grep.out.filtered_fastq, params.adapt)
 
   //########################## MAPPING ##########################
@@ -211,5 +213,6 @@ workflow {
   //###################### QUANTIFICATION #######################
 
   start_position_counts(sort_bam_genome.out.sorted_bam)
+  */
 
 }
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src/nf_modules/concatenate/main.nf

@@ -20,6 +20,6 @@ process concatenate {
     script:
 """
 zcat ${fastq}/*.fastq.gz > merged.fastq
-gzip merged.fastq
+gzip --quiet merged.fastq
 """
 }
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