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BICF
Astrocyte
chipseq_analysis
Commits
ad917147
Commit
ad917147
authored
Mar 28, 2020
by
Venkat Malladi
Browse files
Merge branch '80-concurrent_issue' into ci-merge-test
parents
d7f31c15
fa258f22
Pipeline
#6413
failed with stages
in 247 minutes and 56 seconds
Changes
1
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.gitlab-ci.yml
View file @
ad917147
variables
:
GIT_DEPTH
:
5
GIT_CLONE_PATH
:
$CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_
CONCURRENT_ID/$CI_
PROJECT_NAME/$CI_PIPELINE_ID
GIT_CLONE_PATH
:
$CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME/$CI_PIPELINE_ID
/$CI_CONCURRENT_ID/$CI_JOB_ID/
before_script
:
...
...
@@ -16,6 +16,7 @@ stages:
-
single
-
multiple
-
skip
-
cleanup
user_configuration
:
stage
:
unit
...
...
@@ -29,6 +30,8 @@ astrocyte:
-
module unload nextflow
-
cd ..
-
astrocyte_cli validate chipseq_analysis
after_script
:
-
rm -rf work/
single_end_mouse
:
stage
:
single
...
...
@@ -37,6 +40,8 @@ single_end_mouse:
script
:
-
NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte
true
-
pytest -m singleend
after_script
:
-
rm -rf work/
paired_end_human
:
stage
:
single
...
...
@@ -47,6 +52,8 @@ paired_end_human:
script
:
-
NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd
true
--astrocyte
false
-
pytest -m pairedend
after_script
:
-
rm -rf work/
single_end_single_control
:
stage
:
single
...
...
@@ -57,6 +64,8 @@ single_end_single_control:
script
:
-
NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd
false
--astrocyte
false
-
pytest -m singlecontrol
after_script
:
-
rm -rf work/
single_end_diff
:
stage
:
multiple
...
...
@@ -68,6 +77,8 @@ single_end_diff:
-
NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte
false
-
pytest -m singleend
-
pytest -m singlediff
after_script
:
-
rm -rf work/
paired_end_diff
:
only
:
...
...
@@ -77,6 +88,8 @@ paired_end_diff:
-
NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd
true
--astrocyte
false
-
pytest -m pairedend
-
pytest -m paireddiff
after_script
:
-
rm -rf work/
single_end_skip
:
stage
:
skip
...
...
@@ -85,3 +98,12 @@ single_end_skip:
script
:
-
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
after_script
:
-
rm -rf work/
cleanup_job
:
stage
:
cleanup
script
:
-
cd $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME
-
rm -fr $CI_PIPELINE_ID/
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