update astrocyte to use true false.

.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

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:

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 {