From bf42a0d61bf240bd5c269d13012b6acb98855f32 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@inserm.fr>
Date: Wed, 26 Apr 2023 13:23:41 +0200
Subject: [PATCH] Prepared version to Alia to Test and Training.
---
.gitignore | 6 +++++-
src/bolero.nf | 15 +++++++++------
src/nf_modules/concatenate/main.nf | 2 +-
3 files changed, 15 insertions(+), 8 deletions(-)
diff --git a/.gitignore b/.gitignore
index 289b959..1ead8de 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,6 @@
.nextflow*
-.Rhistory
\ No newline at end of file
+.Rhistory
+work/
+work/*
+bin/*
+results/*
\ No newline at end of file
diff --git a/src/bolero.nf b/src/bolero.nf
index f93670a..f0e8cc3 100755
--- a/src/bolero.nf
+++ b/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)
+ */
}
\ No newline at end of file
diff --git a/src/nf_modules/concatenate/main.nf b/src/nf_modules/concatenate/main.nf
index 05d3170..741d043 100755
--- a/src/nf_modules/concatenate/main.nf
+++ b/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
"""
}
\ No newline at end of file
--
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