diff --git a/docs/basic_training/processes.md b/docs/basic_training/processes.md
index 97deddd2..11251328 100644
--- a/docs/basic_training/processes.md
+++ b/docs/basic_training/processes.md
@@ -223,7 +223,7 @@ The process script can also be defined in a completely dynamic manner using an `
 
 ```groovy linenums="1" title="snippet.nf"
 params.compress = 'gzip'
-params.file2compress = "$baseDir/data/ggal/transcriptome.fa"
+params.file2compress = "$projectDir/data/ggal/transcriptome.fa"
 
 process FOO {
     debug true
@@ -551,8 +551,8 @@ As `ch2` is now a _value_ channel, it can be consumed multiple times and do not
         One possible solution is shown below:
 
         ```groovy linenums="1" title="snippet.nf"
-        params.reads = "$baseDir/data/ggal/*_1.fq"
-        params.transcriptome_file = "$baseDir/data/ggal/transcriptome.fa"
+        params.reads = "$projectDir/data/ggal/*_1.fq"
+        params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
 
         Channel
             .fromPath(params.reads)
@@ -583,7 +583,7 @@ As `ch2` is now a _value_ channel, it can be consumed multiple times and do not
 The `each` qualifier allows you to repeat the execution of a process for each item in a collection every time new data is received. For example:
 
 ```groovy linenums="1" title="snippet.nf"
-sequences = Channel.fromPath("$baseDir/data/ggal/*_1.fq")
+sequences = Channel.fromPath("$projectDir/data/ggal/*_1.fq")
 methods = ['regular', 'espresso']
 
 process ALIGNSEQUENCES {
@@ -624,7 +624,7 @@ In the above example, every time a file of sequences is received as an input by
         Modify the methods list and add another coffee type:
 
         ```groovy linenums="1" title="snippet.nf"
-        sequences = Channel.fromPath("$baseDir/data/ggal/*_1.fq")
+        sequences = Channel.fromPath("$projectDir/data/ggal/*_1.fq")
         methods = ['regular', 'espresso', 'cappuccino']
 
         process ALIGNSEQUENCES {
diff --git a/docs/basic_training/processes.pt.md b/docs/basic_training/processes.pt.md
index f41a18e4..304257bc 100644
--- a/docs/basic_training/processes.pt.md
+++ b/docs/basic_training/processes.pt.md
@@ -188,7 +188,7 @@ O script do processo também pode ser definido de maneira completamente dinâmic
 
 ```groovy linenums="1"
 params.compressor = 'gzip'
-params.arquivo_a_comprimir = "$baseDir/data/ggal/transcriptome.fa"
+params.arquivo_a_comprimir = "$projectDir/data/ggal/transcriptome.fa"
 
 process FOO {
     input:
@@ -347,7 +347,7 @@ workflow {
     ??? solution
 
         ```groovy linenums="1"
-        params.leituras = "$baseDir/data/ggal/*_1.fq"
+        params.leituras = "$projectDir/data/ggal/*_1.fq"
 
         Channel
             .fromPath(params.leituras)
@@ -484,8 +484,8 @@ Isso ocorre porque os canais de valor podem ser consumidos várias vezes e não
     ??? solution
 
         ```groovy linenums="1"
-        params.leituras = "$baseDir/data/ggal/*_1.fq"
-        params.arquivo_transcriptoma = "$baseDir/data/ggal/transcriptome.fa"
+        params.leituras = "$projectDir/data/ggal/*_1.fq"
+        params.arquivo_transcriptoma = "$projectDir/data/ggal/transcriptome.fa"
 
         Channel
             .fromPath(params.leituras)
@@ -548,8 +548,8 @@ No exemplo acima, toda vez que um arquivo de sequências é recebido como entrad
     ??? solution
 
         ```groovy linenums="1"
-        params.leituras = "$baseDir/data/ggal/*_1.fq"
-        params.arquivo_transcriptoma = "$baseDir/data/ggal/transcriptome.fa"
+        params.leituras = "$projectDir/data/ggal/*_1.fq"
+        params.arquivo_transcriptoma = "$projectDir/data/ggal/transcriptome.fa"
         metodos= ['salmon', 'kallisto']
 
         Channel
diff --git a/docs/hands_on/04_implementation.md b/docs/hands_on/04_implementation.md
index d26db870..2f4b7a9b 100644
--- a/docs/hands_on/04_implementation.md
+++ b/docs/hands_on/04_implementation.md
@@ -35,15 +35,15 @@ Edit this file to specify the input files as script parameters. Using this notat
  * Define the default parameters (1)
  */
 
-params.genome     = "${baseDir}/data/genome.fa" // (2)!
-params.variants   = "${baseDir}/data/known_variants.vcf.gz"
-params.blacklist  = "${baseDir}/data/blacklist.bed"
-params.reads      = "${baseDir}/data/reads/ENCSR000COQ1_{1,2}.fastq.gz" // (3)!
+params.genome     = "${projectDir}/data/genome.fa" // (2)!
+params.variants   = "${projectDir}/data/known_variants.vcf.gz"
+params.blacklist  = "${projectDir}/data/blacklist.bed"
+params.reads      = "${projectDir}/data/reads/ENCSR000COQ1_{1,2}.fastq.gz" // (3)!
 params.results    = "results" // (4)!
 ```
 
 1. The `/*`, `*` and `*/` specify comment lines which are ignored by Nextflow.
-2. The `baseDir` variable represents the main script path location.
+2. The `projectDir` variable represents the main script path location.
 3. The `reads` parameter uses a glob pattern to specify the forward (`ENCSR000COQ1_1.fq.gz`) and reverse (`ENCSR000COQ1_2.fq.gz`) reads (paired-end) of a sample.
 4. The `results` parameter is used to specify a directory called `results`.
 
diff --git a/docs/hello_nextflow/03_hello_gatk.md b/docs/hello_nextflow/03_hello_gatk.md
index 956e3a39..19713cc6 100644
--- a/docs/hello_nextflow/03_hello_gatk.md
+++ b/docs/hello_nextflow/03_hello_gatk.md
@@ -143,11 +143,11 @@ process SAMTOOLS_INDEX {
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/hello-nextflow"
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/hello-nextflow"
+$projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/bam/reads_mother.bam"
+params.reads_bam = "${projectDir}/data/bam/reads_mother.bam"
 ```
 
 #### 1.3. Add workflow block to run SAMTOOLS_INDEX
@@ -156,7 +156,7 @@ params.reads_bam = "${baseDir}/data/bam/reads_mother.bam"
 workflow {
 
     // Create input channel (single file via CLI parameter)
-    reads_ch = Channel.from(params.reads_bam)
+    reads_ch = Channel.of(params.reads_bam)
 
     // Create index file for input BAM file
     SAMTOOLS_INDEX(reads_ch)
@@ -227,10 +227,10 @@ process GATK_HAPLOTYPECALLER {
 
 ```groovy title="hello-gatk.nf"
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 ```
 
 #### 2.3. Add a call to the workflow block to run GATK_HAPLOTYPECALLER
@@ -290,9 +290,9 @@ Make the workflow handle multiple samples in bulk.
 ```groovy title="hello-gatk.nf"
 // Primary input
 params.reads_bam = [
-    "${baseDir}/data/bam/reads_mother.bam",
-    "${baseDir}/data/bam/reads_father.bam",
-    "${baseDir}/data/bam/reads_son.bam"
+    "${projectDir}/data/bam/reads_mother.bam",
+    "${projectDir}/data/bam/reads_father.bam",
+    "${projectDir}/data/bam/reads_son.bam"
 ]
 ```
 
@@ -409,9 +409,9 @@ _Before:_
 ```groovy title="hello-gatk.nf"
 // Primary input
 params.reads_bam = [
-    "${baseDir}/data/bam/reads_mother.bam",
-    "${baseDir}/data/bam/reads_father.bam",
-    "${baseDir}/data/bam/reads_son.bam"
+    "${projectDir}/data/bam/reads_mother.bam",
+    "${projectDir}/data/bam/reads_father.bam",
+    "${projectDir}/data/bam/reads_son.bam"
 ]
 ```
 
@@ -419,7 +419,7 @@ _After:_
 
 ```groovy title="hello-gatk.nf"
 // Primary input (list of input files, one per line)
-params.reads_bam = "${baseDir}/data/sample_bams.txt"
+params.reads_bam = "${projectDir}/data/sample_bams.txt"
 ```
 
 #### 4.3. Update the channel factory to read lines from a file
@@ -428,7 +428,7 @@ _Before:_
 
 ```groovy title="hello-gatk.nf"
 // Create input channel
-reads_ch = Channel.from(params.reads_bam)
+reads_ch = Channel.of(params.reads_bam)
 ```
 
 _After:_
@@ -486,14 +486,14 @@ _Before:_
 
 ```groovy title="hello-gatk.nf"
 // Primary input (list of input files, one sample per line)
-params.reads_bam = "${baseDir}/data/bam/sample_bams.txt"
+params.reads_bam = "${projectDir}/data/bam/sample_bams.txt"
 ```
 
 _After:_
 
 ```groovy title="hello-gatk.nf"
 // Primary input (samplesheet in CSV format with ID and file path, one sample per line)
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 ```
 
 #### 5.3. Update the channel factory to parse a CSV file
diff --git a/docs/hello_nextflow/04_hello_modules.md b/docs/hello_nextflow/04_hello_modules.md
index 28a8f588..321fa936 100644
--- a/docs/hello_nextflow/04_hello_modules.md
+++ b/docs/hello_nextflow/04_hello_modules.md
@@ -42,17 +42,17 @@ The pipeline takes in three BAM files, each one containing sequencing data for o
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/hello-nextflow"
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/hello-nextflow"
+$projectDir = params.projectDir
 
 // Primary input (samplesheet in CSV format with ID and file path, one sample per line)
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/docs/hello_nextflow/05_hello_nf-test.md b/docs/hello_nextflow/05_hello_nf-test.md
index ba35e9c4..528dab40 100644
--- a/docs/hello_nextflow/05_hello_nf-test.md
+++ b/docs/hello_nextflow/05_hello_nf-test.md
@@ -169,7 +169,7 @@ _After:_
 ```groovy title="modules/local/samtools/index/tests/main.nf.test" linenums="14"
 process {
     """
-    input[0] = [ [id: 'NA12882' ], file("${baseDir}/data/bam/reads_son.bam") ]
+    input[0] = [ [id: 'NA12882' ], file("${projectDir}/data/bam/reads_son.bam") ]
     """
 }
 ```
@@ -271,7 +271,7 @@ test("reads_mother [bam]") {
         }
         process {
             """
-            input[0] = [ [id: 'NA12878' ], file("${baseDir}/data/bam/reads_mother.bam") ]
+            input[0] = [ [id: 'NA12878' ], file("${projectDir}/data/bam/reads_mother.bam") ]
             """
         }
     }
@@ -295,7 +295,7 @@ test("reads_father [bam]") {
         }
         process {
             """
-            input[0] = [ [id: 'NA12877' ], file("${baseDir}/data/bam/reads_father.bam") ]
+            input[0] = [ [id: 'NA12877' ], file("${projectDir}/data/bam/reads_father.bam") ]
             """
         }
     }
@@ -447,7 +447,7 @@ test("reads_son [bam]") {
             script "../../../samtools/index/main.nf"
             process {
                 """
-                input[0] =  [ [id: 'NA12882' ], file("${baseDir}/data/bam/reads_son.bam") ]
+                input[0] =  [ [id: 'NA12882' ], file("${projectDir}/data/bam/reads_son.bam") ]
                 """
             }
         }
@@ -466,10 +466,10 @@ Then we can refer to the output of that process in the `when` block where we spe
         process {
             """
             input[0] = SAMTOOLS_INDEX.out
-            input[1] = file("${baseDir}/data/ref/ref.fasta")
-            input[2] = file("${baseDir}/data/ref/ref.fasta.fai")
-            input[3] = file("${baseDir}/data/ref/ref.dict")
-            input[4] = file("${baseDir}/data/intervals.list")
+            input[1] = file("${projectDir}/data/ref/ref.fasta")
+            input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
+            input[3] = file("${projectDir}/data/ref/ref.dict")
+            input[4] = file("${projectDir}/data/intervals.list")
             """
         }
     }
@@ -625,7 +625,7 @@ test("reads_mother [bam]") {
             script "../../../samtools/index/main.nf"
             process {
                 """
-                input[0] =  [ [id: 'NA12882' ], file("${baseDir}/data/bam/reads_mother.bam") ]
+                input[0] =  [ [id: 'NA12882' ], file("${projectDir}/data/bam/reads_mother.bam") ]
                 """
             }
         }
@@ -638,10 +638,10 @@ test("reads_mother [bam]") {
         process {
             """
             input[0] = SAMTOOLS_INDEX.out
-            input[1] = file("${baseDir}/data/ref/ref.fasta")
-            input[2] = file("${baseDir}/data/ref/ref.fasta.fai")
-            input[3] = file("${baseDir}/data/ref/ref.dict")
-            input[4] = file("${baseDir}/data/intervals.list")
+            input[1] = file("${projectDir}/data/ref/ref.fasta")
+            input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
+            input[3] = file("${projectDir}/data/ref/ref.dict")
+            input[4] = file("${projectDir}/data/intervals.list")
             """
         }
     }
@@ -664,7 +664,7 @@ test("reads_father [bam]") {
             script "../../../samtools/index/main.nf"
             process {
                 """
-                input[0] =  [ [id: 'NA12882' ], file("${baseDir}/data/bam/reads_father.bam") ]
+                input[0] =  [ [id: 'NA12882' ], file("${projectDir}/data/bam/reads_father.bam") ]
                 """
             }
         }
@@ -677,10 +677,10 @@ test("reads_father [bam]") {
         process {
             """
             input[0] = SAMTOOLS_INDEX.out
-            input[1] = file("${baseDir}/data/ref/ref.fasta")
-            input[2] = file("${baseDir}/data/ref/ref.fasta.fai")
-            input[3] = file("${baseDir}/data/ref/ref.dict")
-            input[4] = file("${baseDir}/data/intervals.list")
+            input[1] = file("${projectDir}/data/ref/ref.fasta")
+            input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
+            input[3] = file("${projectDir}/data/ref/ref.dict")
+            input[4] = file("${projectDir}/data/intervals.list")
             """
         }
     }
@@ -825,12 +825,12 @@ test("family_trio [vcf] [idx]") {
         }
         process {
             """
-            input[0] = file("${baseDir}/modules/local/gatk/jointgenotyping/tests/inputs/family_trio_map.tsv")
+            input[0] = file("${projectDir}/modules/local/gatk/jointgenotyping/tests/inputs/family_trio_map.tsv")
             input[1] = "family_trio"
-            input[2] = file("${baseDir}/data/ref/ref.fasta")
-            input[3] = file("${baseDir}/data/ref/ref.fasta.fai")
-            input[4] = file("${baseDir}/data/ref/ref.dict")
-            input[5] = file("${baseDir}/data/intervals.list")
+            input[2] = file("${projectDir}/data/ref/ref.fasta")
+            input[3] = file("${projectDir}/data/ref/ref.fasta.fai")
+            input[4] = file("${projectDir}/data/ref/ref.dict")
+            input[5] = file("${projectDir}/data/intervals.list")
             """
         }
     }
diff --git a/hands-on/final_main.nf b/hands-on/final_main.nf
index 3722694c..609308da 100644
--- a/hands-on/final_main.nf
+++ b/hands-on/final_main.nf
@@ -2,10 +2,10 @@
  * Define the default parameters
  */
 
-params.genome     = "${baseDir}/data/genome.fa"
-params.variants   = "${baseDir}/data/known_variants.vcf.gz"
-params.blacklist  = "${baseDir}/data/blacklist.bed"
-params.reads      = "${baseDir}/data/reads/ENCSR000C*_{1,2}.fastq.gz"
+params.genome     = "${projectDir}/data/genome.fa"
+params.variants   = "${projectDir}/data/known_variants.vcf.gz"
+params.blacklist  = "${projectDir}/data/blacklist.bed"
+params.reads      = "${projectDir}/data/reads/ENCSR000C*_{1,2}.fastq.gz"
 params.results    = "results"
 
 /*
diff --git a/hello-nextflow/hello-modules.nf b/hello-nextflow/hello-modules.nf
index c942c60f..b0c8f864 100644
--- a/hello-nextflow/hello-modules.nf
+++ b/hello-nextflow/hello-modules.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/nf-training/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/nf-training/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/hello-nextflow/scripts/hello-gatk-1.nf b/hello-nextflow/scripts/hello-gatk-1.nf
index 67033986..e5b5ac73 100644
--- a/hello-nextflow/scripts/hello-gatk-1.nf
+++ b/hello-nextflow/scripts/hello-gatk-1.nf
@@ -3,11 +3,11 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/bam/reads_mother.bam"
+params.reads_bam = "${projectDir}/data/bam/reads_mother.bam"
 
 /*
  * Generate BAM index file
@@ -31,8 +31,8 @@ process SAMTOOLS_INDEX {
 workflow {
 
     // Create input channel
-    reads_ch = Channel.from(params.reads_bam)
+    reads_ch = Channel.of(params.reads_bam)
 
     // Create index file for input BAM file
     SAMTOOLS_INDEX(reads_ch)
-}
\ No newline at end of file
+}
diff --git a/hello-nextflow/scripts/hello-gatk-2.nf b/hello-nextflow/scripts/hello-gatk-2.nf
index 25d31196..99d77be0 100644
--- a/hello-nextflow/scripts/hello-gatk-2.nf
+++ b/hello-nextflow/scripts/hello-gatk-2.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/bam/reads_mother.bam"
+params.reads_bam = "${projectDir}/data/bam/reads_mother.bam"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 /*
  * Generate BAM index file
@@ -66,7 +66,7 @@ process GATK_HAPLOTYPECALLER {
 workflow {
 
     // Create input channel
-    reads_ch = Channel.from(params.reads_bam)
+    reads_ch = Channel.of(params.reads_bam)
 
     // Create index file for input BAM file
     SAMTOOLS_INDEX(reads_ch)
@@ -80,4 +80,4 @@ workflow {
         params.genome_reference_dict,
         params.calling_intervals
     )
-}
\ No newline at end of file
+}
diff --git a/hello-nextflow/scripts/hello-gatk-3.nf b/hello-nextflow/scripts/hello-gatk-3.nf
index 8bf7f1ad..18de2dfa 100644
--- a/hello-nextflow/scripts/hello-gatk-3.nf
+++ b/hello-nextflow/scripts/hello-gatk-3.nf
@@ -3,19 +3,19 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = ["${baseDir}/data/bam/reads_mother.bam",
-                    "${baseDir}/data/bam/reads_father.bam",
-                    "${baseDir}/data/bam/reads_son.bam"]
+params.reads_bam = ["${projectDir}/data/bam/reads_mother.bam",
+                    "${projectDir}/data/bam/reads_father.bam",
+                    "${projectDir}/data/bam/reads_son.bam"]
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 /*
  * Generate BAM index file
@@ -67,7 +67,7 @@ process GATK_HAPLOTYPECALLER {
 workflow {
 
     // Create input channel
-    reads_ch = Channel.from(params.reads_bam)
+    reads_ch = Channel.of(params.reads_bam)
 
     // Create index file for input BAM file
     SAMTOOLS_INDEX(reads_ch)
@@ -80,4 +80,4 @@ workflow {
         params.genome_reference_dict,
         params.calling_intervals
     )
-}
\ No newline at end of file
+}
diff --git a/hello-nextflow/scripts/hello-gatk-4.nf b/hello-nextflow/scripts/hello-gatk-4.nf
index 00dc0f68..1a5abcba 100644
--- a/hello-nextflow/scripts/hello-gatk-4.nf
+++ b/hello-nextflow/scripts/hello-gatk-4.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input (list of input files, one per line)
-params.reads_bam = "${baseDir}/data/sample_bams.txt"
+params.reads_bam = "${projectDir}/data/sample_bams.txt"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 /*
  * Generate BAM index file
diff --git a/hello-nextflow/scripts/hello-gatk-5.nf b/hello-nextflow/scripts/hello-gatk-5.nf
index 8aef43c8..e23ddca4 100644
--- a/hello-nextflow/scripts/hello-gatk-5.nf
+++ b/hello-nextflow/scripts/hello-gatk-5.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input (samplesheet in CSV format with ID and file path, one sample per line)
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 /*
  * Generate BAM index file
diff --git a/hello-nextflow/scripts/hello-gatk-6.nf b/hello-nextflow/scripts/hello-gatk-6.nf
index c942c60f..b0c8f864 100644
--- a/hello-nextflow/scripts/hello-gatk-6.nf
+++ b/hello-nextflow/scripts/hello-gatk-6.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/nf-training/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/nf-training/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/hello-nextflow/scripts/nextflow.config b/hello-nextflow/scripts/nextflow.config
index 0cf2867d..0c950dc1 100644
--- a/hello-nextflow/scripts/nextflow.config
+++ b/hello-nextflow/scripts/nextflow.config
@@ -6,17 +6,17 @@ docker.fixOwnership = true
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/nf-training/hello-nextflow" 
-$baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/nf-training/hello-nextflow" 
+$projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/mkdocs.yml b/mkdocs.yml
index 20642136..c50110ca 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -139,9 +139,6 @@ markdown_extensions:
     - attr_list
     - md_in_html
     - pymdownx.details
-    - pymdownx.emoji:
-          emoji_index: !!python/name:material.extensions.emoji.twemoji
-          emoji_generator: !!python/name:material.extensions.emoji.to_svg
     - pymdownx.highlight:
           anchor_linenums: true
     - pymdownx.inlinehilite
diff --git a/troubleshoot/exercise1/hello-gatk.nf b/troubleshoot/exercise1/hello-gatk.nf
index 0ebe5b8e..b0e6b435 100644
--- a/troubleshoot/exercise1/hello-gatk.nf
+++ b/troubleshoot/exercise1/hello-gatk.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/troubleshoot" 
-baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/troubleshoot" 
+projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/troubleshoot/exercise2/hello-gatk.nf b/troubleshoot/exercise2/hello-gatk.nf
index 17ac5777..0fa52e0b 100644
--- a/troubleshoot/exercise2/hello-gatk.nf
+++ b/troubleshoot/exercise2/hello-gatk.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/troubleshoot" 
-baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/troubleshoot" 
+projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/troubleshoot/exercise3/hello-gatk.nf b/troubleshoot/exercise3/hello-gatk.nf
index a799d06b..83db804c 100644
--- a/troubleshoot/exercise3/hello-gatk.nf
+++ b/troubleshoot/exercise3/hello-gatk.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/troubleshoot" 
-baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/troubleshoot" 
+projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/troubleshoot/exercise4/hello-gatk.nf b/troubleshoot/exercise4/hello-gatk.nf
index fb3212b6..915e3940 100644
--- a/troubleshoot/exercise4/hello-gatk.nf
+++ b/troubleshoot/exercise4/hello-gatk.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/troubleshoot" 
-baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/troubleshoot" 
+projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/troubleshoot/exercise5/hello-gatk.nf b/troubleshoot/exercise5/hello-gatk.nf
index 3a50107d..703259a0 100644
--- a/troubleshoot/exercise5/hello-gatk.nf
+++ b/troubleshoot/exercise5/hello-gatk.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/troubleshoot" 
-baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/troubleshoot" 
+projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"
diff --git a/troubleshoot/hello-gatk.nf b/troubleshoot/hello-gatk.nf
index 0ebe5b8e..b0e6b435 100644
--- a/troubleshoot/hello-gatk.nf
+++ b/troubleshoot/hello-gatk.nf
@@ -3,17 +3,17 @@
  */
 
 // Execution environment setup
-params.baseDir = "/workspace/gitpod/troubleshoot" 
-baseDir = params.baseDir
+params.projectDir = "/workspace/gitpod/troubleshoot" 
+projectDir = params.projectDir
 
 // Primary input
-params.reads_bam = "${baseDir}/data/samplesheet.csv"
+params.reads_bam = "${projectDir}/data/samplesheet.csv"
 
 // Accessory files
-params.genome_reference = "${baseDir}/data/ref/ref.fasta"
-params.genome_reference_index = "${baseDir}/data/ref/ref.fasta.fai"
-params.genome_reference_dict = "${baseDir}/data/ref/ref.dict"
-params.calling_intervals = "${baseDir}/data/intervals.list"
+params.genome_reference = "${projectDir}/data/ref/ref.fasta"
+params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai"
+params.genome_reference_dict = "${projectDir}/data/ref/ref.dict"
+params.calling_intervals = "${projectDir}/data/intervals.list"
 
 // Base name for final output file
 params.cohort_name = "family_trio"