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LBMC
RMI2
RMI2 pipelines
Commits
bb620eb7
Commit
bb620eb7
authored
5 years ago
by
elabaron
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RiboProf.nf & RNAseq.nf : harmonisation and generalisation des termes
parent
38a453b6
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src/RNAseq.nf
+28
-15
28 additions, 15 deletions
src/RNAseq.nf
src/RibosomeProfiling.nf
+22
-10
22 additions, 10 deletions
src/RibosomeProfiling.nf
with
50 additions
and
25 deletions
src/RNAseq.nf
+
28
−
15
View file @
bb620eb7
...
@@ -2,23 +2,24 @@
...
@@ -2,23 +2,24 @@
* RNAseq Analysis pipeline
* RNAseq Analysis pipeline
*/
*/
params
.
input
=
"data/demultiplexed/*{_R1,_R2}.fastq.gz"
params
.
fastq_raw
=
"data/demultiplexed/*{_R1,_R2}.fastq.gz"
params
.
output
=
"results"
Channel
Channel
.
fromFilePairs
(
params
.
input
)
.
fromFilePairs
(
params
.
fastq_raw
)
.
ifEmpty
{
error
"Cannot find any file matching: ${params.
input
}"
}
.
ifEmpty
{
error
"Cannot find any file matching: ${params.
fastq_raw
}"
}
.
set
{
input
_channel
}
.
set
{
fastq_raw
_channel
}
/* Trimming by quality */
/* Trimming by quality */
process
trimming
{
process
trimming
{
tag
"$file_id"
tag
"$file_id"
cpus
4
cpus
4
publishDir
"
results/RNAseq
/01_cutadapt/"
,
mode:
'copy'
publishDir
"
${params.output}
/01_cutadapt/"
,
mode:
'copy'
echo
true
echo
true
input:
input:
set
file_id
,
file
(
reads
)
from
input
_channel
set
file_id
,
file
(
reads
)
from
fastq_raw
_channel
output:
output:
set
file_id
,
"*cut_{R1,R2}.fastq.gz"
into
fastq_files_cut
set
file_id
,
"*cut_{R1,R2}.fastq.gz"
into
fastq_files_cut
...
@@ -51,7 +52,7 @@ Channel
...
@@ -51,7 +52,7 @@ Channel
process
rRNA_removal
{
process
rRNA_removal
{
tag
"$file_id"
tag
"$file_id"
cpus
8
cpus
8
publishDir
"
results/RNAseq
/02_rRNA_depletion/"
,
mode:
'copy'
publishDir
"
${params.output}
/02_rRNA_depletion/"
,
mode:
'copy'
input:
input:
set
file_id
,
file
(
reads
)
from
fastq_files_cut
set
file_id
,
file
(
reads
)
from
fastq_files_cut
...
@@ -62,8 +63,14 @@ process rRNA_removal {
...
@@ -62,8 +63,14 @@ process rRNA_removal {
file
"*.txt"
into
bowtie_report
file
"*.txt"
into
bowtie_report
script:
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> \
-1 ${reads[0]} -2 ${reads[1]} --un-conc-gz ${file_id}_R%.fastq.gz 2> \
${file_id}_bowtie2_report.txt > /dev/null
${file_id}_bowtie2_report.txt > /dev/null
...
@@ -82,7 +89,7 @@ log.info "index : ${params.index_hg38}"
...
@@ -82,7 +89,7 @@ log.info "index : ${params.index_hg38}"
Channel
Channel
.
fromPath
(
params
.
index_hg38
)
.
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
}
.
set
{
index_file_hg38
}
process
hisat2_human
{
process
hisat2_human
{
...
@@ -98,10 +105,16 @@ process hisat2_human {
...
@@ -98,10 +105,16 @@ process hisat2_human {
file
"*.txt"
into
hisat_report
file
"*.txt"
into
hisat_report
script:
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]} \
-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' \
--rna-strandness 'F' \
2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
...
@@ -115,10 +128,10 @@ reads_aligned_hg38.into{for_mapping;for_htseq}
...
@@ -115,10 +128,10 @@ reads_aligned_hg38.into{for_mapping;for_htseq}
process
index_bam
{
process
index_bam
{
tag
"$file_id"
tag
"$file_id"
publishDir
"
results/RNAseq
/03_hisat2
_hg38
/"
,
mode:
'copy'
publishDir
"
${params.output}
/03_hisat2/"
,
mode:
'copy'
input:
input:
set
file_id
,
file
(
bam
)
from
for_mapping
set
file_id
,
file
(
bam
)
from
for_mapping
file
report
from
hisat_report
file
report
from
hisat_report
output:
output:
...
@@ -191,7 +204,7 @@ process sort_bam {
...
@@ -191,7 +204,7 @@ process sort_bam {
"""
"""
samtools sort -@ ${task.cpus} -n -O BAM -o ${file_id}_sorted.bam ${bam}
samtools sort -@ ${task.cpus} -n -O BAM -o ${file_id}_sorted.bam ${bam}
"""
"""
}
}
params
.
gtf
=
"$baseDir/data/annotation/*.gtf"
params
.
gtf
=
"$baseDir/data/annotation/*.gtf"
log
.
info
"gtf files : ${params.gtf}"
log
.
info
"gtf files : ${params.gtf}"
...
@@ -203,7 +216,7 @@ Channel
...
@@ -203,7 +216,7 @@ Channel
process
counting
{
process
counting
{
tag
"$file_id"
tag
"$file_id"
publishDir
"
results/RNAseq
/04_HTseq/"
,
mode:
'copy'
publishDir
"
${params.output}
/04_HTseq/"
,
mode:
'copy'
input:
input:
set
file_id
,
file
(
bam
)
from
sorted_bam_files_2
set
file_id
,
file
(
bam
)
from
sorted_bam_files_2
...
...
This diff is collapsed.
Click to expand it.
src/RibosomeProfiling.nf
+
22
−
10
View file @
bb620eb7
...
@@ -55,8 +55,14 @@ process rRNA_removal {
...
@@ -55,8 +55,14 @@ process rRNA_removal {
file
"*.txt"
into
bowtie_report
file
"*.txt"
into
bowtie_report
script:
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> \
-U - --un-gz ${file_id}_mRNA.fastq.gz 2> \
${file_id}_bowtie2_report.txt > /dev/null
${file_id}_bowtie2_report.txt > /dev/null
...
@@ -75,7 +81,7 @@ log.info "index : ${params.index_hg38}"
...
@@ -75,7 +81,7 @@ log.info "index : ${params.index_hg38}"
Channel
Channel
.
fromPath
(
params
.
index_hg38
)
.
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
}
.
set
{
index_file_hg38
}
process
hisat2_human
{
process
hisat2_human
{
...
@@ -92,9 +98,15 @@ process hisat2_human {
...
@@ -92,9 +98,15 @@ process hisat2_human {
file
"*.txt"
into
hisat_report
file
"*.txt"
into
hisat_report
script:
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} \
-U ${fastq_filtred} --un-gz ${file_id}_notaligned
_hg38
.fastq.gz \
-U ${fastq_filtred} --un-gz ${file_id}_notaligned.fastq.gz \
--end-to-end --rna-strandness 'F' \
--end-to-end --rna-strandness 'F' \
2> ${file_id}_hisat2_hg38.txt | samtools view -bS -F 4 -o ${file_id}.bam
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} \
...
@@ -105,7 +117,7 @@ hisat2 -x genome_tran -p ${task.cpus} \
process
index_bam
{
process
index_bam
{
tag
"$file_id"
tag
"$file_id"
publishDir
"${params.output}/03_hisat2
_hg38
/"
,
mode:
'copy'
publishDir
"${params.output}/03_hisat2/"
,
mode:
'copy'
input:
input:
set
file_id
,
file
(
bam
)
from
reads_aligned_hg38
set
file_id
,
file
(
bam
)
from
reads_aligned_hg38
...
@@ -122,7 +134,7 @@ samtools index ${file_id}_sorted.bam
...
@@ -122,7 +134,7 @@ samtools index ${file_id}_sorted.bam
sorted_bam_files
.
into
{
for_dedup
;
for_htseq
}
sorted_bam_files
.
into
{
for_dedup
;
for_htseq
}
/* deduplicating reads
*/
/* deduplicating reads
params.dedup_options = ""
params.dedup_options = ""
...
@@ -142,11 +154,11 @@ umi_tools dedup -I ${bam[0]} \
...
@@ -142,11 +154,11 @@ umi_tools dedup -I ${bam[0]} \
${params.dedup_options} \
${params.dedup_options} \
-S ${file_id}_dedup.bam > report.txt
-S ${file_id}_dedup.bam > report.txt
"""
"""
}
}
*/
/*
process sort_bam {
process sort_bam {
tag "$file_id"
tag "$file_id"
publishDir
"${params.output}/03_hisat2_
hg38_
dedup/"
,
mode:
'copy'
publishDir "${params.output}/03_hisat2_dedup/", mode: 'copy'
input:
input:
set file_id, file(bam) from dedup_bam
set file_id, file(bam) from dedup_bam
...
@@ -163,7 +175,7 @@ samtools index ${file_id}_sorted.bam
...
@@ -163,7 +175,7 @@ samtools index ${file_id}_sorted.bam
cat ${dedup} > ${file_id}_dedup_report.txt
cat ${dedup} > ${file_id}_dedup_report.txt
"""
"""
}
}
*/
/* HTseq */
/* HTseq */
params
.
gtf
=
"$baseDir/data/annotation/*.gtf"
params
.
gtf
=
"$baseDir/data/annotation/*.gtf"
...
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