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Commit 61a87202 authored by Venkat Malladi's avatar Venkat Malladi
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update astrocyte to use true false.

parent dd5b3b59
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1 merge request!30Resolve "Update Astrocyte documentation and errors"
...@@ -32,7 +32,7 @@ single_end_mouse: ...@@ -32,7 +32,7 @@ single_end_mouse:
only: only:
- master - master
script: script:
- nextflow run workflow/main.nf --astrocyte 'true' -resume - nextflow run workflow/main.nf --astrocyte true -resume
- pytest -m singleend - pytest -m singleend
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -44,7 +44,7 @@ paired_end_human: ...@@ -44,7 +44,7 @@ paired_end_human:
except: except:
- master - master
script: 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 - pytest -m pairedend
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -56,7 +56,7 @@ single_end_diff: ...@@ -56,7 +56,7 @@ single_end_diff:
except: except:
- master - master
script: 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 - pytest -m singlediff
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -66,7 +66,7 @@ paired_end_diff: ...@@ -66,7 +66,7 @@ paired_end_diff:
- master - master
stage: multiple stage: multiple
script: 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 - pytest -m paireddiff
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -76,7 +76,7 @@ single_end_skip: ...@@ -76,7 +76,7 @@ single_end_skip:
only: only:
- master - master
script: 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 - pytest -m singleskip_true
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
...@@ -101,8 +101,8 @@ workflow_parameters: ...@@ -101,8 +101,8 @@ workflow_parameters:
type: select type: select
required: true required: true
choices: choices:
- [ 'true', 'True'] - [ 'true', 'true']
- [ 'false', 'False'] - [ 'false', 'false']
description: | description: |
In single-end sequencing, the sequencer reads a fragment from only one 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 end to the other, generating the sequence of base pairs. In paired-end
...@@ -128,6 +128,24 @@ workflow_parameters: ...@@ -128,6 +128,24 @@ workflow_parameters:
description: | description: |
Reference species and genome used for alignment and subsequent analysis. 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 - id: astrocyte
type: select type: select
choices: choices:
......
...@@ -5,14 +5,14 @@ ...@@ -5,14 +5,14 @@
// Define Input variables // Define Input variables
params.reads = "$baseDir/../test_data/*.fastq.gz" params.reads = "$baseDir/../test_data/*.fastq.gz"
params.pairedEnd = 'false' params.pairedEnd = false
params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt" params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
params.genome = 'GRCm38' params.genome = 'GRCm38'
params.cutoffRatio = 1.2 params.cutoffRatio = 1.2
params.outDir= "$baseDir/output" params.outDir= "$baseDir/output"
params.extendReadsLen = 100 params.extendReadsLen = 100
params.topPeakCount = 600 params.topPeakCount = 600
params.astrocyte = 'false' params.astrocyte = false
params.skipDiff = false params.skipDiff = false
params.skipMotif = false params.skipMotif = false
params.references = "$baseDir/../docs/references.md" params.references = "$baseDir/../docs/references.md"
...@@ -70,12 +70,6 @@ skipMotif = params.skipMotif ...@@ -70,12 +70,6 @@ skipMotif = params.skipMotif
references = params.references references = params.references
multiqc = params.multiqc multiqc = params.multiqc
if (params.pairedEnd == 'false'){
pairedEnd = false
} else {
pairedEnd = true
}
// Check design file for errors // Check design file for errors
process checkDesignFile { process checkDesignFile {
......
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