update scripts remove dsl2 reference

carpentries-incubator · Jun 10, 2024 · fd37bd0 · fd37bd0
1 parent 958c9fa
commit fd37bd0
Show file tree

Hide file tree

Showing 36 changed files with 36 additions and 36 deletions.
diff --git a/episodes/files/scripts/modules/modules_exercise_add_module.nf b/episodes/files/scripts/modules/modules_exercise_add_module.nf
@@ -1,4 +1,4 @@
-nextflow.enable.dsl=2
+
 
 params.reads = "data/yeast/reads/ref1_{1,2}.fq.gz"
 

diff --git a/episodes/files/scripts/parameters/wc-params.nf b/episodes/files/scripts/parameters/wc-params.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 
-nextflow.enable.dsl=2
+
 
 /*  Comments are uninterpreted text included with the script.
     They are useful for describing complex parts of the workflow

diff --git a/episodes/files/scripts/parameters/word_count.nf b/episodes/files/scripts/parameters/word_count.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 
-nextflow.enable.dsl=2
+
 
 /*  Comments are uninterpreted text included with the script.
     They are useful for describing complex parts of the workflow

diff --git a/episodes/files/scripts/process/process_01.nf b/episodes/files/scripts/process/process_01.nf
@@ -1,4 +1,4 @@
-nextflow.enable.dsl=2
+
 
 process NUMSEQ {
   script:

diff --git a/episodes/files/scripts/process/process_conditional.nf b/episodes/files/scripts/process/process_conditional.nf
@@ -1,5 +1,5 @@
 //process_conditional.nf
-nextflow.enable.dsl=2
+
 
 params.method = 'ids'
 params.transcriptome = "$projectDir/data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"

diff --git a/episodes/files/scripts/process/process_escape_bash.nf b/episodes/files/scripts/process/process_escape_bash.nf
@@ -1,5 +1,5 @@
 //process_escape_bash.nf
-nextflow.enable.dsl=2
+
 
 process NUM_IDS {
 

diff --git a/episodes/files/scripts/process/process_exercise_combine.nf b/episodes/files/scripts/process/process_exercise_combine.nf
@@ -1,5 +1,5 @@
 // process_exercise_combine_answer.nf
-nextflow.enable.dsl=2
+
 
 process COMBINE {
  input:

diff --git a/episodes/files/scripts/process/process_exercise_combine_answer.nf b/episodes/files/scripts/process/process_exercise_combine_answer.nf
@@ -1,5 +1,5 @@
 // process_exercise_combine_answer.nf
-nextflow.enable.dsl=2
+
 
 process COMBINE {
  input:

diff --git a/episodes/files/scripts/process/process_exercise_input.nf b/episodes/files/scripts/process/process_exercise_input.nf
@@ -1,5 +1,5 @@
 //process_exercise_input.nf
-nextflow.enable.dsl=2
+
 
 params.chr = "A"
 params.transcriptome = "${projectDir}/data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"

diff --git a/episodes/files/scripts/process/process_exercise_input_answer.nf b/episodes/files/scripts/process/process_exercise_input_answer.nf
@@ -1,4 +1,4 @@
-nextflow.enable.dsl=2
+
 
 params.chr = "A"
 params.transcriptome = "${projectDir}/data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"> >

diff --git a/episodes/files/scripts/process/process_exercise_output.nf b/episodes/files/scripts/process/process_exercise_output.nf
@@ -1,5 +1,5 @@
 //process_exercise_output.nf
-nextflow.enable.dsl=2
+
 
 process EXTRACT_IDS {
   input:

diff --git a/episodes/files/scripts/process/process_exercise_output_answer.nf b/episodes/files/scripts/process/process_exercise_output_answer.nf
@@ -1,5 +1,5 @@
 //process_exercise_output_answer.nf
-nextflow.enable.dsl=2
+
 
 process EXTRACT_IDS {
   input:

diff --git a/episodes/files/scripts/process/process_exercise_publishDir.nf b/episodes/files/scripts/process/process_exercise_publishDir.nf
@@ -1,5 +1,5 @@
 //process_exercise_publishDir.nf
-nextflow.enable.dsl=2
+
 
 params.reads= "data/yeast/reads/ref{1,2,3}*{1,2}.fq.gz"
 

diff --git a/episodes/files/scripts/process/process_exercise_publishDir_answer.nf b/episodes/files/scripts/process/process_exercise_publishDir_answer.nf
@@ -1,5 +1,5 @@
 //process_exercise_publishDir_answer.nf
-nextflow.enable.dsl=2
+
 
 params.reads= "data/yeast/reads/ref{1,2,3}*{1,2}.fq.gz"
 

diff --git a/episodes/files/scripts/process/process_exercise_repeat.nf b/episodes/files/scripts/process/process_exercise_repeat.nf
@@ -1,5 +1,5 @@
 //process_exercise_repeat.nf
- nextflow.enable.dsl=2
+
  process COMBINE {
    input:
    path transcriptome

diff --git a/episodes/files/scripts/process/process_exercise_repeat_answer.nf b/episodes/files/scripts/process/process_exercise_repeat_answer.nf
@@ -1,5 +1,5 @@
 //process_exercise_repeat_answer.nf
-nextflow.enable.dsl=2
+
 
 process COMBINE {
   input:

diff --git a/episodes/files/scripts/process/process_exercise_script_params.nf b/episodes/files/scripts/process/process_exercise_script_params.nf
@@ -1,5 +1,5 @@
 //process_exercise_script_params.nf
-nextflow.enable.dsl=2
+
 
 process COUNT_BASES {
 

diff --git a/episodes/files/scripts/process/process_exercise_script_params_answers.nf b/episodes/files/scripts/process/process_exercise_script_params_answers.nf
@@ -1,5 +1,5 @@
 //process_script_params.nf
-nextflow.enable.dsl=2
+
 
 params.base='A'
 

diff --git a/episodes/files/scripts/process/process_exercise_simple_process.nf b/episodes/files/scripts/process/process_exercise_simple_process.nf
@@ -1,4 +1,4 @@
-nextflow.enable.dsl=2
+
 
 process COUNT_BASES {
 

diff --git a/episodes/files/scripts/process/process_exercise_tuple.nf b/episodes/files/scripts/process/process_exercise_tuple.nf
@@ -1,5 +1,5 @@
 //process_exercise_tuple.nf
-nextflow.enable.dsl=2
+
 
 process COMBINE_REPS {
   input:

diff --git a/episodes/files/scripts/process/process_exercise_tuple_answer.nf b/episodes/files/scripts/process/process_exercise_tuple_answer.nf
@@ -1,5 +1,5 @@
 //process_exercise_tuple_answer.nf
-nextflow.enable.dsl=2
+
 
 process COMBINE_REPS {
   input:

diff --git a/episodes/files/scripts/process/process_input_value.nf b/episodes/files/scripts/process/process_input_value.nf
@@ -1,5 +1,5 @@
 //process_input_value.nf
-nextflow.enable.dsl=2
+
 
 process PRINTCHR {
 

diff --git a/episodes/files/scripts/process/process_multi_line.nf b/episodes/files/scripts/process/process_multi_line.nf
@@ -1,5 +1,5 @@
 //process_multi_line.nf
-nextflow.enable.dsl=2
+
 
 process NUMSEQ_CHR {
     script:

diff --git a/episodes/files/scripts/process/process_output_file.nf b/episodes/files/scripts/process/process_output_file.nf
@@ -1,5 +1,5 @@
 //process_output_file.nf
-nextflow.enable.dsl=2
+
 
 params.transcriptome="${projectDir}/data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"
 

diff --git a/episodes/files/scripts/process/process_output_multiple.nf b/episodes/files/scripts/process/process_output_multiple.nf
@@ -1,5 +1,5 @@
 //process_output_multiple.nf
-nextflow.enable.dsl=2
+
 
 params.transcriptome="${projectDir}/data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"
 

diff --git a/episodes/files/scripts/process/process_output_value.nf b/episodes/files/scripts/process/process_output_value.nf
@@ -1,5 +1,5 @@
 //process_output_value.nf
-nextflow.enable.dsl=2
+
 
 params.transcriptome="${projectDir}/data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"
 

diff --git a/episodes/files/scripts/process/process_publishDir.nf b/episodes/files/scripts/process/process_publishDir.nf
@@ -1,5 +1,5 @@
 //process_publishDir.nf
-nextflow.enable.dsl=2
+
 
 process COMBINE_READS {
   publishDir "results/merged_reads"

diff --git a/episodes/files/scripts/process/process_publishDir_semantic.nf b/episodes/files/scripts/process/process_publishDir_semantic.nf
@@ -1,5 +1,5 @@
 //process_publishDir_semantic.nf
-nextflow.enable.dsl=2
+
 
 params.transcriptome="${projectDir}/data/yeast/transcriptome/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz"
 

diff --git a/episodes/files/scripts/process/process_python_script.nf b/episodes/files/scripts/process/process_python_script.nf
@@ -1,5 +1,5 @@
 //process_python_script.nf
-nextflow.enable.dsl=2
+
 
 process PROCESS_READS {
 

diff --git a/episodes/files/scripts/process/process_script.nf b/episodes/files/scripts/process/process_script.nf
@@ -1,5 +1,5 @@
 //process_script.nf
-nextflow.enable.dsl=2
+
 
 chr = "A"
 

diff --git a/episodes/files/scripts/process/process_script_params.nf b/episodes/files/scripts/process/process_script_params.nf
@@ -1,5 +1,5 @@
 //process_script_params.nf
-nextflow.enable.dsl=2
+
 
 params.chr = "A"
 

diff --git a/episodes/files/scripts/process/process_shell.nf b/episodes/files/scripts/process/process_shell.nf
@@ -1,5 +1,5 @@
 //process_shell.nf
-nextflow.enable.dsl=2
+
 
 process NUM_IDS {
 

diff --git a/episodes/files/scripts/process/process_simple.nf b/episodes/files/scripts/process/process_simple.nf
@@ -1,4 +1,4 @@
-nextflow.enable.dsl=2
+
 
 process COUNT_BASES {
 

diff --git a/episodes/files/scripts/process/process_tuple_io.nf b/episodes/files/scripts/process/process_tuple_io.nf
@@ -1,5 +1,5 @@
 //process_tuple_io.nf
-nextflow.enable.dsl=2
+
 
 process COMBINE_FQ {
   input:

diff --git a/episodes/files/scripts/process/process_tuple_io_fastp.nf b/episodes/files/scripts/process/process_tuple_io_fastp.nf
@@ -1,5 +1,5 @@
 //process_tuple_io_fastp.nf
-nextflow.enable.dsl=2
+
 
 process FASTP {
   input:

diff --git a/episodes/files/scripts/workflow/workflow_01.nf b/episodes/files/scripts/workflow/workflow_01.nf
@@ -1,5 +1,5 @@
 //workflow_01.nf
-nextflow.enable.dsl=2
+
 
 
  process FASTQC {