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Commit fb686f83 authored by elabaron's avatar elabaron
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src/RNAseq.nf : cosmetic changes

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......@@ -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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