From 3cf06f92604cc89c2ff51a0f8ff7cfe67752f871 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 22 Apr 2019 14:57:05 -0500
Subject: [PATCH] Move single-end to run on astrocyte.
---
.gitlab-ci.yml | 2 +-
astrocyte_pkg.yml | 2 +-
workflow/main.nf | 6 +++---
3 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 282e1f4..72521f9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -32,7 +32,7 @@ single_end_mouse:
only:
- master
script:
- - nextflow run workflow/main.nf --astrocyte 'false' -resume
+ - nextflow run workflow/main.nf --astrocyte 'true' -resume
- pytest -m singleend
artifacts:
expire_in: 2 days
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 4118a74..1b71610 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -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
diff --git a/workflow/main.nf b/workflow/main.nf
index a00ec57..f10e577 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -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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