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chipseq_analysis
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Astrocyte
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BICF
chipseq_analysis
Commits
3cf06f92
Commit
3cf06f92
authored
5 years ago
by
Venkat Malladi
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Move single-end to run on astrocyte.
parent
abeaa753
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.gitlab-ci.yml
+1
-1
1 addition, 1 deletion
.gitlab-ci.yml
astrocyte_pkg.yml
+1
-1
1 addition, 1 deletion
astrocyte_pkg.yml
workflow/main.nf
+3
-3
3 additions, 3 deletions
workflow/main.nf
with
5 additions
and
5 deletions
.gitlab-ci.yml
+
1
−
1
View file @
3cf06f92
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@@ -32,7 +32,7 @@ single_end_mouse:
only
:
-
master
script
:
-
nextflow run workflow/main.nf --astrocyte '
fals
e' -resume
-
nextflow run workflow/main.nf --astrocyte '
tru
e' -resume
-
pytest -m singleend
artifacts
:
expire_in
:
2 days
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astrocyte_pkg.yml
+
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−
1
View file @
3cf06f92
...
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@@ -108,7 +108,7 @@ workflow_parameters:
end to the other, generating the sequence of base pairs. In paired-end
reading it starts at one read, finishes this direction at the specified
read length, and then starts another round of reading from the opposite
end of the fragment.
end of the fragment.
(Paired-end: True, Single-end: False)
-
id
:
design
type
:
file
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workflow/main.nf
+
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−
3
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3cf06f92
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@@ -22,9 +22,9 @@ params.multiqc = "$baseDir/conf/multiqc_config.yaml"
if (params.astrocyte) {
print("Running under astrocyte")
referenceLocation = "/project/shared/bicf_workflow_ref"
params.bwaIndex = "$referenceLocation/$genome"
params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
params.fasta = "$referenceLocation/$genome/genome.fa.txt"
params.bwaIndex = "$referenceLocation/$
params.
genome"
params.chromSizes = "$referenceLocation/$
params.
genome/genomefile.txt"
params.fasta = "$referenceLocation/$
params.
genome/genome.fa.txt"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.genomeSize = 'hs'
} else if (params.chromSizes == 'GRCm38') {
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