diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 73aaf7b2482d05ee04b9428606378b2575e7c46a..084b9ff2e84260fddfe215d13913faacb4f2c191 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -2,23 +2,24 @@
* RNAseq Analysis pipeline
*/
-params.input = "data/demultiplexed/*{_R1,_R2}.fastq.gz"
+params.fastq_raw = "data/demultiplexed/*{_R1,_R2}.fastq.gz"
+params.output = "results"
Channel
- .fromFilePairs(params.input)
- .ifEmpty { error "Cannot find any file matching: ${params.input}" }
- .set {input_channel}
+ .fromFilePairs(params.fastq_raw)
+ .ifEmpty { error "Cannot find any file matching: ${params.fastq_raw}" }
+ .set {fastq_raw_channel}
/* Trimming by quality */
process trimming {
tag "$file_id"
cpus 4
- publishDir "results/RNAseq/01_cutadapt/", mode: 'copy'
+ publishDir "${params.output}/01_cutadapt/", mode: 'copy'
echo true
input:
- set file_id, file(reads) from input_channel
+ set file_id, file(reads) from fastq_raw_channel
output:
set file_id, "*cut_{R1,R2}.fastq.gz" into fastq_files_cut
@@ -51,7 +52,7 @@ Channel
process rRNA_removal {
tag "$file_id"
cpus 8
- publishDir "results/RNAseq/02_rRNA_depletion/", mode: 'copy'
+ publishDir "${params.output}/02_rRNA_depletion/", mode: 'copy'
input:
set file_id, file(reads) from fastq_files_cut
@@ -62,8 +63,14 @@ process rRNA_removal {
file "*.txt" into bowtie_report
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
-bowtie2 --sensitive -p ${task.cpus} -x human_rRNA_tRNA \
+bowtie2 --sensitive -p ${task.cpus} -x ${index_id} \
-1 ${reads[0]} -2 ${reads[1]} --un-conc-gz ${file_id}_R%.fastq.gz 2> \
${file_id}_bowtie2_report.txt > /dev/null
@@ -82,7 +89,7 @@ log.info "index : ${params.index_hg38}"
Channel
.fromPath ( params.index_hg38 )
- .ifEmpty { error "Cannot find any hg38 index files matching: ${params.index_hg38}" }
+ .ifEmpty { error "Cannot find any index files matching: ${params.index_hg38}" }
.set { index_file_hg38 }
process hisat2_human {
@@ -98,10 +105,16 @@ process hisat2_human {
file "*.txt" into hisat_report
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.ht2/ && !(index_file =~ /.*\.rev\.1\.ht2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.ht2/)[0][1]
+ }
+ }
"""
-hisat2 -x genome_tran -p ${task.cpus} \
+hisat2 -x ${index_id} -p ${task.cpus} \
-1 ${fastq_filtred[0]} -2 ${fastq_filtred[1]} \
---un-conc-gz ${file_id}_notaligned_hg38_R%.fastq.gz \
+--un-conc-gz ${file_id}_notaligned_R%.fastq.gz \
--rna-strandness 'F' \
2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
@@ -115,10 +128,10 @@ reads_aligned_hg38.into{for_mapping;for_htseq}
process index_bam {
tag "$file_id"
- publishDir "results/RNAseq/03_hisat2_hg38/", mode: 'copy'
+ publishDir "${params.output}/03_hisat2/", mode: 'copy'
input:
- set file_id, file(bam) from for_mapping
+ set file_id, file(bam) from for_mapping
file report from hisat_report
output:
@@ -191,7 +204,7 @@ process sort_bam {
"""
samtools sort -@ ${task.cpus} -n -O BAM -o ${file_id}_sorted.bam ${bam}
"""
-}
+}
params.gtf = "$baseDir/data/annotation/*.gtf"
log.info "gtf files : ${params.gtf}"
@@ -203,7 +216,7 @@ Channel
process counting {
tag "$file_id"
- publishDir "results/RNAseq/04_HTseq/", mode: 'copy'
+ publishDir "${params.output}/04_HTseq/", mode: 'copy'
input:
set file_id, file(bam) from sorted_bam_files_2
diff --git a/src/RibosomeProfiling.nf b/src/RibosomeProfiling.nf
index 15e02098a462d9a5c7126218b3364106ee53da4d..9586d01e71ab885c4a733c8d439eb3c388352491 100644
--- a/src/RibosomeProfiling.nf
+++ b/src/RibosomeProfiling.nf
@@ -55,8 +55,14 @@ process rRNA_removal {
file "*.txt" into bowtie_report
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+ }
+ }
"""
-zcat ${reads} | bowtie2 --sensitive -p ${task.cpus} -x human_rRNA_tRNA \
+zcat ${reads} | bowtie2 --sensitive -p ${task.cpus} -x ${index_id} \
-U - --un-gz ${file_id}_mRNA.fastq.gz 2> \
${file_id}_bowtie2_report.txt > /dev/null
@@ -75,7 +81,7 @@ log.info "index : ${params.index_hg38}"
Channel
.fromPath ( params.index_hg38 )
- .ifEmpty { error "Cannot find any hg38 index files matching: ${params.index_hg38}" }
+ .ifEmpty { error "Cannot find any index files matching: ${params.index_hg38}" }
.set { index_file_hg38 }
process hisat2_human {
@@ -92,9 +98,15 @@ process hisat2_human {
file "*.txt" into hisat_report
script:
+ index_id = index[0]
+ for (index_file in index) {
+ if (index_file =~ /.*\.1\.ht2/ && !(index_file =~ /.*\.rev\.1\.ht2/)) {
+ index_id = ( index_file =~ /(.*)\.1\.ht2/)[0][1]
+ }
+ }
"""
-hisat2 -x genome_tran -p ${task.cpus} \
--U ${fastq_filtred} --un-gz ${file_id}_notaligned_hg38.fastq.gz \
+hisat2 -x ${index_id} -p ${task.cpus} \
+-U ${fastq_filtred} --un-gz ${file_id}_notaligned.fastq.gz \
--end-to-end --rna-strandness 'F' \
2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
@@ -105,7 +117,7 @@ hisat2 -x genome_tran -p ${task.cpus} \
process index_bam {
tag "$file_id"
- publishDir "${params.output}/03_hisat2_hg38/", mode: 'copy'
+ publishDir "${params.output}/03_hisat2/", mode: 'copy'
input:
set file_id, file(bam) from reads_aligned_hg38
@@ -122,7 +134,7 @@ samtools index ${file_id}_sorted.bam
sorted_bam_files.into{for_dedup;for_htseq}
-/* deduplicating reads */
+/* deduplicating reads
params.dedup_options = ""
@@ -142,11 +154,11 @@ umi_tools dedup -I ${bam[0]} \
${params.dedup_options} \
-S ${file_id}_dedup.bam > report.txt
"""
-}
-
+}*/
+/*
process sort_bam {
tag "$file_id"
- publishDir "${params.output}/03_hisat2_hg38_dedup/", mode: 'copy'
+ publishDir "${params.output}/03_hisat2_dedup/", mode: 'copy'
input:
set file_id, file(bam) from dedup_bam
@@ -163,7 +175,7 @@ samtools index ${file_id}_sorted.bam
cat ${dedup} > ${file_id}_dedup_report.txt
"""
}
-
+*/
/* HTseq */
params.gtf = "$baseDir/data/annotation/*.gtf"