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BICF
Astrocyte
chipseq_analysis
Commits
92ea443a
Commit
92ea443a
authored
Mar 28, 2020
by
Venkat Malladi
Browse files
Add Nextflow opts.
parent
e09a8b62
Pipeline
#6405
failed with stages
in 22 minutes and 19 seconds
Changes
1
Pipelines
1
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.gitlab-ci.yml
View file @
92ea443a
...
...
@@ -30,7 +30,7 @@ single_end_mouse:
only
:
-
master
script
:
-
nextflow run workflow/main.nf --astrocyte
true
-
NXF_OPTS="-Dleveldb.mmap=false"
nextflow run workflow/main.nf --astrocyte
true
-
pytest -m singleend
paired_end_human
:
...
...
@@ -40,7 +40,7 @@ paired_end_human:
except
:
-
master
script
:
-
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd
true
--astrocyte
false
-
NXF_OPTS="-Dleveldb.mmap=false"
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd
true
--astrocyte
false
-
pytest -m pairedend
single_end_single_control
:
...
...
@@ -50,7 +50,7 @@ single_end_single_control:
except
:
-
master
script
:
-
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd
false
--astrocyte
false
-
NXF_OPTS="-Dleveldb.mmap=false"
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd
false
--astrocyte
false
-
pytest -m singlecontrol
single_end_diff
:
...
...
@@ -60,7 +60,7 @@ single_end_diff:
except
:
-
master
script
:
-
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte
false
-
NXF_OPTS="-Dleveldb.mmap=false"
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte
false
-
pytest -m singleend
-
pytest -m singlediff
...
...
@@ -69,7 +69,7 @@ paired_end_diff:
-
master
stage
:
multiple
script
:
-
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd
true
--astrocyte
false
-
NXF_OPTS="-Dleveldb.mmap=false"
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd
true
--astrocyte
false
-
pytest -m pairedend
-
pytest -m paireddiff
...
...
@@ -78,5 +78,5 @@ single_end_skip:
only
:
-
master
script
:
-
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff
true
--skipMotif
true
--skipPlotProfile
true
--astrocyte
false
-
NXF_OPTS="-Dleveldb.mmap=false"
nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff
true
--skipMotif
true
--skipPlotProfile
true
--astrocyte
false
-
pytest -m singleskip_true
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