update all other processes to dsl 2 syntax

Author: junjun-zhang

tools/extract-files-from-tarball/extract-files-from-tarball.nf

@@ -21,7 +21,7 @@
  * author Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 params.tarball = ""
 params.pattern = ""

tools/extract-files-from-tarball/tests/checker.nf

@@ -21,12 +21,12 @@
  * author Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 params.tarball = "data/test.caveman.tgz"
 params.pattern = "flagged.muts"
 
-include extractFilesFromTarball from "../extract-files-from-tarball"
+include { extractFilesFromTarball } from "../extract-files-from-tarball"
 
 workflow {
   main:
@@ -35,8 +35,4 @@ workflow {
       params.pattern
     )
 
-  publish:
-    extractFilesFromTarball.out.output_file to: 'outdir', overwrite: true
-    extractFilesFromTarball.out.output_file_index to: 'outdir', overwrite: true
-    extractFilesFromTarball.out.extracted_files to: 'outdir', overwrite: true
 }

tools/payload-gen-dna-alignment/payload-gen-dna-alignment.nf

@@ -23,7 +23,7 @@
  *   Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 version = '0.3.1.0'
 
 params.files_to_upload = ""

tools/payload-gen-dna-alignment/tests/checker.nf

@@ -23,15 +23,15 @@
  *   Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 params.files_to_upload = ""
 params.seq_experiment_analysis = ""
 params.read_group_ubam_analysis = "NO_FILE"
 params.wf_name = ""
 params.wf_version = ""
 
-include payloadGenDnaAlignment from "../payload-gen-dna-alignment" params(params)
+include { payloadGenDnaAlignment } from "../payload-gen-dna-alignment" params(params)
 
 workflow {
   main:
@@ -42,7 +42,4 @@ workflow {
       params.wf_name,
       params.wf_version
     )
-  publish:
-    payloadGenDnaAlignment.out.payload to: 'outdir', overwrite: true
-    payloadGenDnaAlignment.out.alignment_files to: 'outdir', overwrite: true
 }

tools/payload-gen-read-group-ubam/payload-gen-read-group-ubam.nf

@@ -22,7 +22,7 @@
  *         Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 version = "0.1.2.0"
 
 params.sequencing_experiment_analysis = ""
@@ -68,7 +68,4 @@ workflow {
       params.wf_short_name,
       params.wf_version
     )
-
-  publish:
-    payloadGenReadGroupUbam.out.payload to: 'outdir', overwrite: true
 }

tools/payload-gen-read-group-ubam/tests/checker.nf

@@ -21,15 +21,15 @@
  * author Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 params.sequencing_experiment_analysis = ""
 params.ubam = ""
 params.wf_name = ""
 params.wf_short_name = ""
 params.wf_version = ""
 
-include "../payload-gen-read-group-ubam" params(params)
+include {payloadGenReadGroupUbam} from "../payload-gen-read-group-ubam" params(params)
 
 
 workflow {
@@ -41,7 +41,4 @@ workflow {
       params.wf_short_name,
       params.wf_version
     )
-
-  publish:
-    payloadGenReadGroupUbam.out.payload to: 'outdir', overwrite: true
 }

tools/payload-gen-seq-experiment/payload-gen-seq-experiment.nf

@@ -21,7 +21,7 @@
  * Author Linda Xiang <linda.xiang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 version = '0.1.3.0'
 
 params.user_submit_metadata = ""

tools/payload-gen-seq-experiment/tests/checker.nf

@@ -21,14 +21,14 @@
  * author Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 params.user_submit_metadata = ""
 params.wf_name = ""
 params.wf_short_name = ""
 params.wf_version = ""
 
-include "../payload-gen-seq-experiment" params(params)
+include {payloadGenSeqExperiment} from "../payload-gen-seq-experiment" params(params)
 
 workflow {
   main:
@@ -39,6 +39,4 @@ workflow {
       params.wf_version,
       'ok'
     )
-  publish:
-    payloadGenSeqExperiment.out.payload to: 'outdir', mode: 'copy', overwrite: true
 }

tools/payload-generation/payload-generation.nf

@@ -21,7 +21,7 @@
  * author Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 params.bundle_type = ""
 params.payload_schema_version = ""

tools/payload-generation/tests/checker.nf

@@ -21,7 +21,7 @@
  * author Junjun Zhang <junjun.zhang@oicr.on.ca>
  */
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 params.bundle_type = "dna_alignment"
 params.payload_schema_version = "0.1.0-rc.2"
@@ -35,7 +35,7 @@ params.analysis_input_payload = [
 params.wf_short_name = ""
 params.wf_version = ""
 
-include "../payload-generation" params(params)
+include {payloadGeneration; getSecondaryFile} from "../payload-generation" params(params)
 
 Channel
   .fromPath(params.analysis_input_payload, checkIfExists: false)
@@ -53,6 +53,4 @@ workflow {
       params.wf_short_name,
       params.wf_version
     )
-  publish:
-    payloadGeneration.out.payload to: 'outdir', mode: 'copy', overwrite: true
 }