From 61a87202f07d7540406db20b28613a699e51f8fc Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 22 Apr 2019 21:07:09 -0500
Subject: [PATCH] update astrocyte to use true false.
---
.gitlab-ci.yml | 10 +++++-----
astrocyte_pkg.yml | 22 ++++++++++++++++++++--
workflow/main.nf | 10 ++--------
3 files changed, 27 insertions(+), 15 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 72521f9..128756e 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 'true' -resume
+ - nextflow run workflow/main.nf --astrocyte true -resume
- pytest -m singleend
artifacts:
expire_in: 2 days
@@ -44,7 +44,7 @@ paired_end_human:
except:
- master
script:
- - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte 'false' -resume
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
- pytest -m pairedend
artifacts:
expire_in: 2 days
@@ -56,7 +56,7 @@ single_end_diff:
except:
- master
script:
- - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte 'false' -resume
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false -resume
- pytest -m singlediff
artifacts:
expire_in: 2 days
@@ -66,7 +66,7 @@ paired_end_diff:
- master
stage: multiple
script:
- - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte 'false' -resume
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
- pytest -m paireddiff
artifacts:
expire_in: 2 days
@@ -76,7 +76,7 @@ single_end_skip:
only:
- master
script:
- - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --astrocyte 'false' -resume
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --astrocyte false -resume
- pytest -m singleskip_true
artifacts:
expire_in: 2 days
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 1b71610..2c040e8 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -101,8 +101,8 @@ workflow_parameters:
type: select
required: true
choices:
- - [ 'true', 'True']
- - [ 'false', 'False']
+ - [ 'true', 'true']
+ - [ 'false', 'false']
description: |
In single-end sequencing, the sequencer reads a fragment from only one
end to the other, generating the sequence of base pairs. In paired-end
@@ -128,6 +128,24 @@ workflow_parameters:
description: |
Reference species and genome used for alignment and subsequent analysis.
+ - id: skipDiff
+ type: select
+ required: true
+ choices:
+ - [ 'true', 'true']
+ - [ 'false', 'false']
+ description: |
+ Run differential peak analysis
+
+ - id: skipMotif
+ type: select
+ required: true
+ choices:
+ - [ 'true', 'true']
+ - [ 'false', 'false']
+ description: |
+ Run motif calling
+
- id: astrocyte
type: select
choices:
diff --git a/workflow/main.nf b/workflow/main.nf
index eb809f3..b0d60c6 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -5,14 +5,14 @@
// Define Input variables
params.reads = "$baseDir/../test_data/*.fastq.gz"
-params.pairedEnd = 'false'
+params.pairedEnd = false
params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
params.genome = 'GRCm38'
params.cutoffRatio = 1.2
params.outDir= "$baseDir/output"
params.extendReadsLen = 100
params.topPeakCount = 600
-params.astrocyte = 'false'
+params.astrocyte = false
params.skipDiff = false
params.skipMotif = false
params.references = "$baseDir/../docs/references.md"
@@ -70,12 +70,6 @@ skipMotif = params.skipMotif
references = params.references
multiqc = params.multiqc
-if (params.pairedEnd == 'false'){
- pairedEnd = false
-} else {
- pairedEnd = true
-}
-
// Check design file for errors
process checkDesignFile {
--
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