From 92ea443abf2235f2212f0aa70042e65dd133bf52 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 28 Mar 2020 09:53:28 -0500
Subject: [PATCH] Add Nextflow opts.
---
.gitlab-ci.yml | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c5a0ec4..5a9c93c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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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