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GUDMAP_RBK
RNA-seq
Commits
3add27fa
Commit
3add27fa
authored
4 years ago
by
Gervaise Henry
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Remove local executor from aws config
parent
f9e50ab2
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1 merge request
!81
Develop
Pipeline
#9747
passed with stages
in 29 minutes and 49 seconds
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2 changed files
docs/nxf_aws-ci-test.json
+1
-1
1 addition, 1 deletion
docs/nxf_aws-ci-test.json
nextflowConf/aws.config
+0
-16
0 additions, 16 deletions
nextflowConf/aws.config
with
1 addition
and
17 deletions
docs/nxf_aws-ci-test.json
+
1
−
1
View file @
3add27fa
[
"utsw-bicf/gudmap_rbk.rna-seq"
,
"-r"
,
"develop"
,
"-profile"
,
"aws"
,
"--deriva"
,
"s3://bicf-nf-output/ci-env/auth/credential.json"
,
"--bdbag"
,
"s3://bicf-nf-output/ci-env/auth/cookies.txt"
,
"--repRID"
,
"Q-Y5F6"
,
"--source"
,
"staging"
,
"--upload"
,
"false"
,
"--dev"
,
"false"
,
"--ci"
,
"true"
,
"--refSource"
,
"datahub"
,
"--outDir"
,
"s3://bicf-nf-output/ci-env/output/Q-Y5F6_fastqoverride"
,
"--fastqsForce"
,
"s3://bicf-nf-output/ci-env/input/*.fastq.gz"
]
[
"utsw-bicf/gudmap_rbk.rna-seq"
,
"-r"
,
"develop"
,
"-profile"
,
"aws"
,
"--deriva"
,
"s3://bicf-nf-output/ci-env/auth/credential.json"
,
"--bdbag"
,
"s3://bicf-nf-output/ci-env/auth/cookies.txt"
,
"--repRID"
,
"Q-Y5F6"
,
"--source"
,
"staging"
,
"--upload"
,
"false"
,
"--dev"
,
"false"
,
"--ci"
,
"true"
,
"--refSource"
,
"datahub"
,
"--outDir"
,
"s3://bicf-nf-output/ci-env/output/Q-Y5F6_fastqoverride"
,
"--fastqsForce"
,
"s3://bicf-nf-output/ci-env/input/*.fastq.gz"
]
\ No newline at end of file
This diff is collapsed.
Click to expand it.
nextflowConf/aws.config
+
0
−
16
View file @
3add27fa
...
...
@@ -4,12 +4,10 @@ params {
process
{
withName
:
trackStart
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
getBag
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
...
...
@@ -18,7 +16,6 @@ process {
memory
=
'32 GB'
}
withName
:
parseMetadata
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
...
...
@@ -35,7 +32,6 @@ process {
memory
=
'32 GB'
}
withName
:
seqwho
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
...
...
@@ -44,7 +40,6 @@ process {
memory
=
'32 GB'
}
withName
:
downsampleData
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
...
...
@@ -61,7 +56,6 @@ process {
memory
=
'32 GB'
}
withName
:
checkMetadata
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
...
...
@@ -86,52 +80,42 @@ process {
memory
=
'32 GB'
}
withName
:
aggrQC
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
uploadInputBag
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
uploadExecutionRun
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
uploadQC
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
uploadProcessedFile
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
uploadOutputBag
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
finalizeExecutionRun
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
failPreExecutionRun
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
failExecutionRun
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
withName
:
uploadQC_fail
{
executor
=
'local'
cpus
=
1
memory
=
'1 GB'
}
...
...
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