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chipseq_analysis
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BICF
Astrocyte
chipseq_analysis
Commits
eb8e3e73
Commit
eb8e3e73
authored
6 years ago
by
Venkat Malladi
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Update to be astrocyte compatible.
parent
7b79b436
1 merge request
!25
Resolve "Test Astrocyte"
Pipeline
#3559
failed with stages
in 11 seconds
Changes
2
Pipelines
1
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2 changed files
astrocyte_pkg.yml
+12
-13
12 additions, 13 deletions
astrocyte_pkg.yml
workflow/main.nf
+11
-9
11 additions, 9 deletions
workflow/main.nf
with
23 additions
and
22 deletions
astrocyte_pkg.yml
+
12
−
13
View file @
eb8e3e73
...
@@ -51,6 +51,7 @@ workflow_modules:
...
@@ -51,6 +51,7 @@ workflow_modules:
-
'
UCSC_userApps/v317'
-
'
UCSC_userApps/v317'
-
'
R/3.3.2-gccmkl'
-
'
R/3.3.2-gccmkl'
-
'
meme/4.11.1-gcc-openmpi'
-
'
meme/4.11.1-gcc-openmpi'
-
'
pandoc/2.7'
# A list of parameters used by the workflow, defining how to present them,
# A list of parameters used by the workflow, defining how to present them,
...
@@ -93,7 +94,7 @@ workflow_parameters:
...
@@ -93,7 +94,7 @@ workflow_parameters:
description
:
|
description
:
|
One or more input FASTQ files from a ChIP-seq expereiment and a design
One or more input FASTQ files from a ChIP-seq expereiment and a design
file with the link bewetwen the same file name and sample id
file with the link bewetwen the same file name and sample id
regex
:
"
.*(fastq|fq)*"
regex
:
"
.*(fastq|fq)*
gz
"
min
:
2
min
:
2
-
id
:
pairedEnd
-
id
:
pairedEnd
...
@@ -115,7 +116,7 @@ workflow_parameters:
...
@@ -115,7 +116,7 @@ workflow_parameters:
description
:
|
description
:
|
A design file listing sample id, fastq files, corresponding control id
A design file listing sample id, fastq files, corresponding control id
and additional information about the sample.
and additional information about the sample.
regex
:
"
.*t
sv
"
regex
:
"
.*t
xt
"
-
id
:
genome
-
id
:
genome
type
:
select
type
:
select
...
@@ -128,12 +129,14 @@ workflow_parameters:
...
@@ -128,12 +129,14 @@ workflow_parameters:
Reference species and genome used for alignment and subsequent analysis.
Reference species and genome used for alignment and subsequent analysis.
-
id
:
astrocyte
-
id
:
astrocyte
type
:
string
type
:
select
required
:
true
choices
:
default
:
'
true'
-
[
'
true'
,
'
true'
]
regex
:
"
true"
required
:
true
description
:
|
default
:
'
true'
Ensure configuraton for astrocyte
description
:
|
Ensure configuraton for astrocyte.
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
...
@@ -154,8 +157,4 @@ vizapp_cran_packages:
...
@@ -154,8 +157,4 @@ vizapp_cran_packages:
# List of any Bioconductor packages, not provided by the modules,
# List of any Bioconductor packages, not provided by the modules,
# that must be made available to the vizapp
# that must be made available to the vizapp
vizapp_bioc_packages
:
vizapp_bioc_packages
:
[]
-
none
vizapp_github_packages
:
-
js229/Vennerable
This diff is collapsed.
Click to expand it.
workflow/main.nf
+
11
−
9
View file @
eb8e3e73
...
@@ -7,6 +7,7 @@
...
@@ -7,6 +7,7 @@
params.reads = "$baseDir/../test_data/*.fastq.gz"
params.reads = "$baseDir/../test_data/*.fastq.gz"
params.pairedEnd = 'false'
params.pairedEnd = 'false'
params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
params.genome = 'GRCm38'
params.cutoffRatio = 1.2
params.cutoffRatio = 1.2
params.outDir= "$baseDir/output"
params.outDir= "$baseDir/output"
params.extendReadsLen = 100
params.extendReadsLen = 100
...
@@ -17,25 +18,26 @@ params.skipMotif = false
...
@@ -17,25 +18,26 @@ params.skipMotif = false
params.references = "$baseDir/../docs/references.md"
params.references = "$baseDir/../docs/references.md"
// Assign variables if astrocyte
// Assign variables if astrocyte
params.genome = 'GRCm38'
if (params.astrocyte) {
if (params.astrocyte == 'false') {
print("Running under astrocyte")
params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
} else if (params.astrocyte == 'true') {
referenceLocation = "/project/shared/bicf_workflow_ref"
referenceLocation = "/project/shared/bicf_workflow_ref"
params.bwaIndex = "$referenceLocation/$genome"
params.bwaIndex = "$referenceLocation/$genome"
params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
params.fasta = "$referenceLocation/$genome/genome.fa.txt"
params.fasta = "$referenceLocation/$genome/genome.fa.txt"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.
chr
omSize
s
= 'hs'
params.
gen
om
e
Size = 'hs'
} else if (params.chromSizes == 'GRCm38') {
} else if (params.chromSizes == 'GRCm38') {
params.
chr
omSize
s
= 'mm'
params.
gen
om
e
Size = 'mm'
}
}
} else {
params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
}
}
// Check inputs
// Check inputs
if( params.bwaIndex ){
if( params.bwaIndex ){
bwaIndex = Channel
bwaIndex = Channel
...
...
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