All files to nextflow.enable.dsl=2

- Resolves #253
vib-singlecell-nf · Jan 15, 2021 · 5041068 · 5041068
1 parent 0f1ad1b
commit 5041068
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diff --git a/main.nf b/main.nf
@@ -1,6 +1,6 @@
 import static groovy.json.JsonOutput.*
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include { 
     INIT;

diff --git a/main_atac.nf b/main_atac.nf
@@ -1,6 +1,6 @@
 import static groovy.json.JsonOutput.*
 
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include { 
     INIT;

diff --git a/src/archr/processes/cell_calling.nf b/src/archr/processes/cell_calling.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/archr/bin/" : ""
 

diff --git a/src/archr/processes/createArrow_unfiltered.nf b/src/archr/processes/createArrow_unfiltered.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/archr/bin/" : ""
 

diff --git a/src/bap/processes/barcode_multiplet.nf b/src/bap/processes/barcode_multiplet.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : ""
 

diff --git a/src/bap/processes/biorad_debarcode.nf b/src/bap/processes/biorad_debarcode.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : ""
 

diff --git a/src/bap/workflows/bap_debarcode.nf b/src/bap/workflows/bap_debarcode.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  Import sub-workflows from the modules:

diff --git a/src/bwamaptools/main.nf b/src/bwamaptools/main.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/bwamaptools/processes/add_barcode_as_tag.nf b/src/bwamaptools/processes/add_barcode_as_tag.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 // binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : ""
 

diff --git a/src/bwamaptools/processes/index.nf b/src/bwamaptools/processes/index.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 // binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : ""
 

diff --git a/src/bwamaptools/processes/mapping.nf b/src/bwamaptools/processes/mapping.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 // binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : ""
 

diff --git a/src/bwamaptools/processes/mapping_summary.nf b/src/bwamaptools/processes/mapping_summary.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/bwamaptools/bin/" : ""
 

diff --git a/src/celda/main.nf b/src/celda/main.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 // Should be set in case this pipeline is run with other pipelines (e.g.: single_sample)
 

diff --git a/src/celda/main.test.nf b/src/celda/main.test.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include { 
     INIT;

diff --git a/src/celda/processes/runDecontX.nf b/src/celda/processes/runDecontX.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/celda/processes/utils.nf b/src/celda/processes/utils.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/celda/workflows/decontX.nf b/src/celda/workflows/decontX.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 ////////////////////////////////////////////////////////
 //  Import sub-workflows/processes from the utils module:

diff --git a/src/cellranger-atac/main.nf b/src/cellranger-atac/main.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 // include groupParams from '../../utils/utils.nf'
 

diff --git a/src/cellranger-atac/processes/count.nf b/src/cellranger-atac/processes/count.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 toolParams = params.sc.cellranger_atac
 

diff --git a/src/cellranger-atac/processes/mkfastq.nf b/src/cellranger-atac/processes/mkfastq.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 toolParams = params.sc.cellranger_atac
 

diff --git a/src/cellranger-atac/workflows/cellRangerCountWithMetadata.nf b/src/cellranger-atac/workflows/cellRangerCountWithMetadata.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/cellranger/main.nf b/src/cellranger/main.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  Define the parameters for current testing proces

diff --git a/src/cellranger/processes/count.nf b/src/cellranger/processes/count.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include {
     isParamNull;

diff --git a/src/cellranger/processes/mkfastq.nf b/src/cellranger/processes/mkfastq.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 toolParams = params.sc.cellranger
 

diff --git a/src/cellranger/processes/utils.nf b/src/cellranger/processes/utils.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 if(!params.containsKey("test")) {
     binDir = "${workflow.projectDir}/src/cellranger/bin/"

diff --git a/src/cellranger/workflows/cellRangerCountWithLibraries.nf b/src/cellranger/workflows/cellRangerCountWithLibraries.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/cellranger/workflows/cellRangerCountWithMetadata.nf b/src/cellranger/workflows/cellRangerCountWithMetadata.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/cellranger/workflows/cellranger_libraries.nf b/src/cellranger/workflows/cellranger_libraries.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/cellranger/workflows/mkfastq.nf b/src/cellranger/workflows/mkfastq.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  Define the parameters for current testing proces

diff --git a/src/channels/channels.nf b/src/channels/channels.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include {
     getOutsChannel as getTenXCellRangerOutsChannel;

diff --git a/src/channels/file.nf b/src/channels/file.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include {
     extractSample

diff --git a/src/channels/singleend.nf b/src/channels/singleend.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 def extractSample(path) {
     pattern = /(.+)\/(.+)_R[1-2](.*)\.fastq(\.gz)?/

diff --git a/src/channels/sra.nf b/src/channels/sra.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 workflow getChannel {
 

diff --git a/src/channels/tenx.nf b/src/channels/tenx.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 CELLRANGER_OUTS_REGEX = /(.+)\/(.+)\/outs/
 CELLRANGER_H5_REGEX = /(.+)\/(.+)\/outs\/(.+)\.h5/

diff --git a/src/directs/main.test.nf b/src/directs/main.test.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include {
     SC__DIRECTS__SELECT_DEFAULT_CLUSTERING

diff --git a/src/directs/processes/selectDefaultClustering.nf b/src/directs/processes/selectDefaultClustering.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/directs/bin/" : ""
 

diff --git a/src/dropletutils/processes/barcode_selection.nf b/src/dropletutils/processes/barcode_selection.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROPLET_UTILS__BARCODE_SELECTION {
 

diff --git a/src/dropseqtools/processes/bam_tag_histogram.nf b/src/dropseqtools/processes/bam_tag_histogram.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__BAM_TAG_HISTOGRAM {
 

diff --git a/src/dropseqtools/processes/convert_to_ref_flat.nf b/src/dropseqtools/processes/convert_to_ref_flat.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__CONVERT_TO_REFFLAT {
 

diff --git a/src/dropseqtools/processes/detect_bead_synthesis_errors.nf b/src/dropseqtools/processes/detect_bead_synthesis_errors.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__DETECT_REPAIR_BARCODE_SYNTHESIS_ERRORS {
 

diff --git a/src/dropseqtools/processes/digital_expression.nf b/src/dropseqtools/processes/digital_expression.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__DIGITAL_EXPRESSION {
 

diff --git a/src/dropseqtools/processes/filter_bam.nf b/src/dropseqtools/processes/filter_bam.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__FILTER_UNALIGNED_TAGGED_BAM {
 

diff --git a/src/dropseqtools/processes/gzip.nf b/src/dropseqtools/processes/gzip.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process GZIP {
 

diff --git a/src/dropseqtools/processes/polya_trimmer.nf b/src/dropseqtools/processes/polya_trimmer.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__TRIM_POLYA_UNALIGNED_TAGGED_TRIMMED_SMART {
 

diff --git a/src/dropseqtools/processes/tag_read_with_gene_exon.nf b/src/dropseqtools/processes/tag_read_with_gene_exon.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__TAG_READ_WITH_GENE_EXON {
 

diff --git a/src/dropseqtools/processes/trim_starting_sequence.nf b/src/dropseqtools/processes/trim_starting_sequence.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process SC__DROP_SEQ_TOOLS__TRIM_SMART_UNALIGNED_TAGGED_FILTERED_BAM {
 

diff --git a/src/edirect/processes/sra_metadata.nf b/src/edirect/processes/sra_metadata.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process EDIRECT__SRAID_TO_SAMPLENAME {
 

diff --git a/src/edirect/workflows/sra_fastq_urls.nf b/src/edirect/workflows/sra_fastq_urls.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 include {
     EDIRECT__SRAID_TO_SAMPLENAME

diff --git a/src/fastp/processes/clean_and_fastqc.nf b/src/fastp/processes/clean_and_fastqc.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 /**
  * Preprocess + FastQC

diff --git a/src/flybaser/processes/convertNomenclature.nf b/src/flybaser/processes/convertNomenclature.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 if(!params.containsKey("test")) {
     binDir = "${workflow.projectDir}/src/flybaser/bin/"

diff --git a/src/harmony/processes/runHarmony.nf b/src/harmony/processes/runHarmony.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/harmony/bin/" : ""
 

diff --git a/src/harmony/workflows/bec_harmony.nf b/src/harmony/workflows/bec_harmony.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  process imports:

diff --git a/src/harmony/workflows/harmony_only.nf b/src/harmony/workflows/harmony_only.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  process imports:

diff --git a/src/pcacv/processes/runPCACV.nf b/src/pcacv/processes/runPCACV.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import java.nio.file.Paths
 

diff --git a/src/picard/processes/create_sequence_dictionary.nf b/src/picard/processes/create_sequence_dictionary.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process PICARD__CREATE_SEQUENCE_DICTIONARY {
 

diff --git a/src/picard/processes/fastq_to_bam.nf b/src/picard/processes/fastq_to_bam.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process PICARD__FASTQ_TO_BAM {
 

diff --git a/src/picard/processes/merge_bam_alignment.nf b/src/picard/processes/merge_bam_alignment.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process PICARD__MERGE_BAM_ALIGNMENT {
 

diff --git a/src/picard/processes/sam_to_fastq.nf b/src/picard/processes/sam_to_fastq.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process PICARD__BAM_TO_FASTQ {
 

diff --git a/src/picard/processes/sort_sam.nf b/src/picard/processes/sort_sam.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 process PICARD__SORT_SAM {
 

diff --git a/src/popscle/main.nf b/src/popscle/main.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  Import sub-workflows from the modules:

diff --git a/src/popscle/processes/demuxlet.nf b/src/popscle/processes/demuxlet.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/popscle/bin/" : ""
 

diff --git a/src/popscle/processes/dsc_pileup.nf b/src/popscle/processes/dsc_pileup.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/popscle/bin/" : ""
 

diff --git a/src/popscle/workflows/demuxlet.nf b/src/popscle/workflows/demuxlet.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  Import sub-workflows from the modules:

diff --git a/src/popscle/workflows/dsc_pileup.nf b/src/popscle/workflows/dsc_pileup.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 //////////////////////////////////////////////////////
 //  Import sub-workflows from the modules:

diff --git a/src/pycistopic/processes/macs2_call_peaks.nf b/src/pycistopic/processes/macs2_call_peaks.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 // binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : ""
 

diff --git a/src/scanpy/main.nf b/src/scanpy/main.nf
@@ -1,4 +1,4 @@
-nextflow.preview.dsl=2
+nextflow.enable.dsl=2
 
 import static groovy.json.JsonOutput.*