Commit 61a87202 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

update astrocyte to use true false.

parent dd5b3b59
......@@ -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
......@@ -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:
......
......@@ -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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