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GeT-nextflow-NGL-Bi
wf-Illumina-nf
Merge requests
!16
FastQ namming using NGL api
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Merged
FastQ namming using NGL api
dev_Jules
into
master
Overview
0
Commits
2
Pipelines
1
Changes
9
Merged
Jules Sabban
requested to merge
dev_Jules
into
master
10 months ago
Overview
0
Commits
2
Pipelines
1
Changes
9
Expand
Name of fastq with info from NGL databases
Uniformity with ng6 file names (new pipeline option)
Add files to readsets
Move MD5SUM process from CORE_PIPELINE to ILLUMINA_QC workflow
ref:
#91 (closed)
0
0
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master
master (base)
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latest version
latest version
6a7302f8
2 commits,
10 months ago
9 files
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71
−
27
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9
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conf/base.config
+
13
−
3
Options
@@ -125,12 +125,15 @@ process {
withLabel
:
bwa
{
module
=
toolsModuleHash
[
'BWA'
]
cpus
= {
checkMax
(
6
*
task
.
attempt
,
'cpus'
) }
memory
= {
checkMax
(
8
.
GB
*
task
.
attempt
,
'memory'
) }
memory
= {
checkMax
(
16
.
GB
*
task
.
attempt
,
'memory'
) }
time
= {
checkMax
(
3
.
d
*
task
.
attempt
,
'time'
) }
publishDir
= [
path
:
"${params.outdir}/alignment/bwa"
,
mode
:
'copy'
mode
: {
if
(
params
.
DTM_mode
)
'symlink'
else
'copy'
}
]
}
@@ -207,6 +210,13 @@ process {
}
withName
:
FILE_RENAME
{
ext
.
args
= [
params
.
run_date
?
"--date "
+
params
.
run_date
:
''
,
params
.
ng6_name
?
"--ng6_like"
:
''
,
].
join
(
' '
)
}
// -----
WithLabel
withLabel
:
littleJob
{
executor
=
'local'
@@ -216,7 +226,7 @@ process {
module
=
toolsModuleHash
[
'SAMTOOLS'
]
cpus
= {
checkMax
(
6
*
task
.
attempt
,
'cpus'
) }
memory
= {
checkMax
(
8
.
GB
*
task
.
attempt
,
'memory'
) }
time
= {
checkMax
(
3
.
h
*
task
.
attempt
,
'time'
) }
time
= {
checkMax
(
24
.
h
*
task
.
attempt
,
'time'
) }
}
withLabel
:
alignment
{
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