Fix #336 baseDir -> projectDir, from -> of

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 {

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

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`.
 

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"
 ]
 ```
 
@@ -409,17 +409,17 @@ _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"
 ]
 ```
 
 _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

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"

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")
             """
         }
     }

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"
 
 /*

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"