From fb686f830aae8b9fee26dfbac5d963cabbddd824 Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Mon, 28 Sep 2020 11:21:11 +0200
Subject: [PATCH] src/RNAseq.nf : cosmetic changes
---
src/RNAseq.nf | 110 +++++++++++++++++++++++++++++++++++---------------
1 file changed, 78 insertions(+), 32 deletions(-)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 2b940d89..54064704 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -2,18 +2,41 @@
* RNAseq Analysis pipeline
*/
+//////////////////////////////////////////////////////
+// PARAMETERS //
+//////////////////////////////////////////////////////
+
+///////////////////////
+// PARMS : FILE PATH //
+///////////////////////
+
params.fastq_raw = "data/fastq/*{_R1,_R2}.fastq.gz"
params.output = "results"
-params.do_fastqc = true
-//params.script_cov = "src/norm_coverage.sh"
params.filter = "data/filter/human_rRNA_tRNA/*.bt2"
params.index_genome = "data/genome/*.ht2"
-params.do_dedup = true
params.gtf = "data/annotation/*.gtf"
params.gtf_collapse = "data/annotation/*.gtf"
params.index_postgenome = "data/post_genome/*.ht2"
+
+/////////////////////
+// PARMS : OPTIONS //
+/////////////////////
+
+params.do_fastqc = true
+params.do_dedup = true
params.do_postgenome = true
+////////////////////////
+// ADAPTORS SEQUENCES //
+////////////////////////
+
+params.adaptorR1 = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"
+params.adaptorR2 = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
+
+//////////////
+// LOG INFO //
+//////////////
+
log.info "input raw : ${params.fastq_raw}"
log.info "outut directory : ${params.output}"
log.info "filter index files : ${params.filter}"
@@ -27,6 +50,10 @@ log.info "do deduplication ? : ${params.do_dedup}"
log.info "do post genome alignement ? : ${params.do_postgenome}"
log.info ""
+//////////////
+// CHANNELS //
+//////////////
+
Channel
.fromFilePairs(params.fastq_raw)
.ifEmpty { error "Cannot find any file matching: ${params.fastq_raw}" }
@@ -58,7 +85,18 @@ Channel
.ifEmpty { error "Cannot find any index files matching: ${params.index_postgenome}" }
.set { POSTGENOME_INDEX }
+//////////////////////////////////////////////////////
+// PROCESS //
+//////////////////////////////////////////////////////
+
+////////////////////////////////////////////////////////////////////////
+//////////////////////////// PRE PROCESS ///////////////////////////////
+////////////////////////////////////////////////////////////////////////
+
+
+/////////////////////////
/* Fastqc of raw input */
+/////////////////////////
process fastqc_raw {
tag "$file_id"
@@ -77,7 +115,10 @@ process fastqc_raw {
fastqc ${file_id}* -t ${task.cpus}
"""
}
+
+///////////////////////
/* Trimming adaptors */
+///////////////////////
process trimming {
tag "$file_id"
@@ -119,7 +160,10 @@ process trimming {
CUTADAPT_OUTPUT.into{CUTADAPT_OUTPUT_FASTQC;
CUTADAPT_OUTPUT_FILTER}
+
+/////////////////////////
/* Fastqc of raw input */
+/////////////////////////
process fastqc_cut {
tag "$file_id"
@@ -139,7 +183,9 @@ process fastqc_cut {
"""
}
+/////////////////////////////
/* rRNA and tRNA filtering */
+/////////////////////////////
process rRNA_removal {
tag "$file_id"
@@ -181,7 +227,9 @@ FILTER_FASTQ.into{FILTER_FASTQ_FASTQC;
FILTER_FASTQ_POSTGENOME
}
+/////////////////////////////
/* Fastqc of filtred reads */
+/////////////////////////////
process fastqc_filter {
tag "$file_id"
@@ -201,7 +249,15 @@ process fastqc_filter {
"""
}
+
+///////////////////////////////////////////////////////////////////
+//////////////////////////// GENOME ///////////////////////////////
+///////////////////////////////////////////////////////////////////
+
+
+///////////////////////////////////////////////
/* mapping against human genome with hisat2 */
+///////////////////////////////////////////////
process hisat2_human {
tag "$file_id"
@@ -245,8 +301,9 @@ fi
HISAT_ALIGNED.into{HISAT_ALIGNED_FASTQC;
HISAT_ALIGNED_DEDUP}
-
+////////////////////////////
/* Fastqc of genome reads */
+////////////////////////////
process fastqc_genome {
tag "$file_id"
@@ -266,7 +323,9 @@ process fastqc_genome {
"""
}
+////////////////////////////
/* Deduplication of reads */
+////////////////////////////
process dedup_genome {
tag "$file_id"
@@ -297,7 +356,9 @@ DEDUP_GENOME.into{DEDUP_GENOME_HTSEQ;
DEDUP_GENOME_RNASEQC
}
-/* HTseq */
+///////////
+/* HTseq */
+///////////
process sort_bam {
tag "$file_id"
@@ -348,7 +409,9 @@ htseq-count ${bam[0]} ${gtf} \
"""
}
-/* HTseq */
+///////////////
+/* RNASEQ QC */
+///////////////
process rnaseq_qc {
tag "$file_id"
@@ -372,8 +435,9 @@ rnaseqc ${gtf} ${bam[0]} -s ${file_id} ./ \
//////////////////////////// POST GENOME ///////////////////////////////
////////////////////////////////////////////////////////////////////////
-
+/////////////////////////
/* HISAT2 POST_GENOMIC */
+/////////////////////////
process hisat2_postGenomic {
tag "$file_id"
@@ -418,7 +482,9 @@ fi
POSTGENOME_ALIGNED.into{POSTGENOME_ALIGNED_FASTQC;
POSTGENOME_ALIGNED_DEDUP}
+////////////////////////////
/* Deduplication of reads */
+////////////////////////////
process dedup_postgenome {
tag "$file_id"
@@ -459,34 +525,14 @@ process fastqc_postgenome {
"""
}
-/*
-Channel
- .fromFilePairs(params.script_cov)
- .ifEmpty { error "Cannot find any file matching: ${params.script_cov}" }
- .set {script_channel}
-
-process coverage {
- tag "$file_id"
- publishDir "${params.output}/05_coverage/", mode: 'copy'
-
- input:
- set file_id, file(bam) from sorted_bam_coverage
- set script from script_channel.collect()
-
- output:
- file "*.bw" into coverage_files
+////////////////////////////////////////////////////////////////////////
+//////////////////////////// POST PROCESS //////////////////////////////
+////////////////////////////////////////////////////////////////////////
- script:
-"""
-bash ${script} -b ${bam} \
- -o {file_id}.bw \
- --binSize 1 \
- -p ${cpus} 8
-"""
-}
-*/
+/////////////
/* MultiQC */
+/////////////
process multiqc {
--
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