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LBMC
nextflow
Commits
b867bf9a
Verified
Commit
b867bf9a
authored
4 years ago
by
Laurent Modolo
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bowtie: update to match CONTRIBUTING.md
parent
1f72b2c4
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src/nf_modules/bowtie/main.nf
+51
-38
51 additions, 38 deletions
src/nf_modules/bowtie/main.nf
with
51 additions
and
38 deletions
src/nf_modules/bowtie/main.nf
+
51
−
38
View file @
b867bf9a
...
...
@@ -2,17 +2,21 @@ version = "1.2.2"
container_url
=
"lbmc/bowtie:${version}"
params
.
index_fasta
=
""
params
.
index_fasta_out
=
""
process
index_fasta
{
container
=
"${container_url}"
label
"big_mem_multi_cpus"
tag
"$fasta.baseName"
tag
"$file_id"
if
(
params
.
index_fasta_out
!=
""
)
{
publishDir
"results/${params.index_fasta_out}"
,
mode:
'copy'
}
input:
path
fasta
tuple
val
(
file_id
),
path
(
fasta
)
output:
path
"*.index*"
,
emit:
index
path
"*_report.txt"
,
emit:
report
tuple
val
(
file_id
),
path
(
"*.index*"
)
,
emit:
index
tuple
val
(
file_id
),
path
(
"*_report.txt"
)
,
emit:
report
script:
"""
...
...
@@ -27,57 +31,66 @@ fi
"""
}
params
.
mapping_fastq
=
""
params
.
mapping_fastq
=
"--very-sensitive"
params
.
mapping_fastq_out
=
""
process
mapping_fastq
{
container
=
"${container_url}"
label
"big_mem_multi_cpus"
tag
"$pair_id"
if
(
params
.
mapping_fastq_out
!=
""
)
{
publishDir
"results/${params.mapping_fastq_out}"
,
mode:
'copy'
}
input:
path
index
tuple
val
(
pair
_id
),
path
(
reads
)
tuple
val
(
index_id
),
path
(
index
)
tuple
val
(
file
_id
),
path
(
reads
)
output:
tuple
val
(
pair
_id
),
path
(
"*.bam"
),
emit:
bam
tuple
val
(
file
_id
),
path
(
"*.bam"
),
emit:
bam
path
"*_report.txt"
,
emit:
report
script:
if
(
file_id
instanceof
List
){
file_prefix
=
file_id
[
0
]
}
else
{
file_prefix
=
file_id
}
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
]
}
}
if
(
reads
instanceof
List
)
"""
# -v specify the max number of missmatch, -k the number of match reported per
# reads
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${
pair
_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${
pair
_id}.bam
if grep -q "Error" ${
pair
_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${
pair
_id}_bowtie_report_tmp.txt > \
${
pair
_id}_bowtie_mapping_report.txt
"""
else
"""
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq}
-q ${reads} 2> \
${file_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
${file_id}_bowtie_mapping_report.txt
"""
if
(
reads
.
size
()
==
2
)
"""
# -v specify the max number of missmatch, -k the number of match reported per
# reads
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${
file
_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${
file
_id}.bam
if grep -q "Error" ${
file
_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${
file
_id}_bowtie_report_tmp.txt > \
${
file
_id}_bowtie_mapping_report.txt
"""
else
if
(
reads
.
size
()
==
1
)
"""
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq}
-q ${reads} 2> \
${file_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
${file_id}_bowtie_mapping_report.txt
"""
}
params
.
mapping_fastq_pairedend
=
""
...
...
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