diff --git a/main.nf b/main.nf index 951bea55..9efa3aaf 100644 --- 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 index 0d381c70..a3f7762a 100644 --- 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 index db08eca3..cdff4674 100644 --- 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") ? "${workflow.projectDir}/src/archr/bin/" : "" diff --git a/src/archr/processes/createArrow_unfiltered.nf b/src/archr/processes/createArrow_unfiltered.nf index 5b20af98..c82cac6e 100644 --- a/src/archr/processes/createArrow_unfiltered.nf +++ b/src/archr/processes/createArrow_unfiltered.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/archr/bin/" : "" diff --git a/src/bap/processes/barcode_multiplet.nf b/src/bap/processes/barcode_multiplet.nf index 48cbbeda..578aaa49 100644 --- 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") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/bap/processes/biorad_debarcode.nf b/src/bap/processes/biorad_debarcode.nf index 381fdeed..8fc438b2 100644 --- a/src/bap/processes/biorad_debarcode.nf +++ b/src/bap/processes/biorad_debarcode.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/bap/workflows/bap_debarcode.nf b/src/bap/workflows/bap_debarcode.nf index 5e40e529..00934604 100644 --- 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 index 1b6eacba..56b85c16 100644 --- 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 index 647e65dc..474cdbc9 100644 --- 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") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/bwamaptools/processes/index.nf b/src/bwamaptools/processes/index.nf index 48e3ffce..9ae964e9 100644 --- a/src/bwamaptools/processes/index.nf +++ b/src/bwamaptools/processes/index.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 // binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/bwamaptools/processes/mapping.nf b/src/bwamaptools/processes/mapping.nf index dad8be3e..d82ef45a 100644 --- 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") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/bwamaptools/processes/mapping_summary.nf b/src/bwamaptools/processes/mapping_summary.nf index 1703374d..3517efad 100644 --- a/src/bwamaptools/processes/mapping_summary.nf +++ b/src/bwamaptools/processes/mapping_summary.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/bwamaptools/bin/" : "" diff --git a/src/celda/main.nf b/src/celda/main.nf index c96ed573..7eb95c0a 100644 --- 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 index 30be2558..10d8f1b6 100644 --- 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 index 109955e7..0c749555 100644 --- 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 index b8742b96..0cecc6f7 100644 --- 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 index e8afdd49..17c74af7 100644 --- 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 index ea278503..52ae94f6 100644 --- 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 index bfb9c608..7d28ffd5 100644 --- 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 index cddebb5c..3694039a 100644 --- 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 index 44432a17..b0850e1d 100644 --- 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 index 2519f7df..6854e2ec 100644 --- 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 index fda72ce1..845bb7fe 100644 --- 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 index ecbd9954..85e23da4 100644 --- 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 index a0e736f2..2dbe14c4 100644 --- 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 index e9f7e7df..9835ed3a 100644 --- 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 index 39f4f7e8..3fd6fc31 100644 --- 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 index 1c06ad4e..b7c78c65 100644 --- 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 index 28c0ae2f..229e73d4 100644 --- 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 index b8da023f..99b589d8 100644 --- 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 index f51f866c..e017b07c 100644 --- 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 index 721ad9c6..c2f717aa 100644 --- 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 index eaab85e4..7d7dd37d 100644 --- 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 index debc6077..5c5a6168 100644 --- 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 index b7f2a5ed..677b76a3 100644 --- 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 index 2894f91a..ea600809 100644 --- 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 index 8ae5d147..c4f10d03 100644 --- 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 index e08aabca..38e8489e 100644 --- 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 index b0efe5f9..ee91ad93 100644 --- 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 index 1dc40f4b..22d875bc 100644 --- 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 index 60faaf3b..755fd548 100644 --- 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 index b3a9bc07..d99b02e4 100644 --- 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 index 66fd9b27..d17e149a 100644 --- 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 index b2c0c1f5..dd6cdef7 100644 --- 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 index f512cf0d..20a227bc 100644 --- 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 index 72c25797..58436846 100644 --- 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 index 31f75407..49a8f6c8 100644 --- 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 index cf375e09..883ef89b 100644 --- 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 index f1281f9c..3550b84c 100644 --- 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 index 1b9c1ea1..7db1134c 100644 --- 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 = "${workflow.projectDir}/src/flybaser/bin/" diff --git a/src/harmony/processes/runHarmony.nf b/src/harmony/processes/runHarmony.nf index b2b6c24e..d2884598 100644 --- a/src/harmony/processes/runHarmony.nf +++ b/src/harmony/processes/runHarmony.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/harmony/bin/" : "" diff --git a/src/harmony/workflows/bec_harmony.nf b/src/harmony/workflows/bec_harmony.nf index 5fc40244..44345a0f 100644 --- 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 index 5b858ab2..63a0d756 100644 --- 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 index f12a69d1..6a7dc94e 100644 --- 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 index 6ea1f02f..4b638ead 100644 --- 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 index 593b14e9..e97dcd99 100644 --- 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 index 7eb2ff4f..b19a9b27 100644 --- 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 index 2defe85c..ee87f02d 100644 --- 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 index 0ef076ed..32acc056 100644 --- 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 index c701aa10..3a814a9d 100644 --- 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 index 493ea8c3..07f79e09 100644 --- 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") ? "${workflow.projectDir}/src/popscle/bin/" : "" diff --git a/src/popscle/processes/dsc_pileup.nf b/src/popscle/processes/dsc_pileup.nf index 3df63672..c7c0bde7 100644 --- a/src/popscle/processes/dsc_pileup.nf +++ b/src/popscle/processes/dsc_pileup.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/popscle/bin/" : "" diff --git a/src/popscle/workflows/demuxlet.nf b/src/popscle/workflows/demuxlet.nf index 34f82feb..d6212d92 100644 --- 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 index 24ba349a..d360ac14 100644 --- 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 index 4930c9bc..ff43cef2 100644 --- 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") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/scanpy/main.nf b/src/scanpy/main.nf index 6d0b4cd7..e0e10ff9 100644 --- a/src/scanpy/main.nf +++ b/src/scanpy/main.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import static groovy.json.JsonOutput.* diff --git a/src/scanpy/main.test.nf b/src/scanpy/main.test.nf index 548b7e16..656f7d52 100644 --- a/src/scanpy/main.test.nf +++ b/src/scanpy/main.test.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 /////////////////////////////////////////// // Define the parameters for all processes diff --git a/src/scanpy/processes/batch_effect_correct.nf b/src/scanpy/processes/batch_effect_correct.nf index 3ff66836..a1822719 100644 --- a/src/scanpy/processes/batch_effect_correct.nf +++ b/src/scanpy/processes/batch_effect_correct.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scanpy/bin/" : "" diff --git a/src/scanpy/processes/cluster.nf b/src/scanpy/processes/cluster.nf index eafd19cc..24bce01b 100644 --- a/src/scanpy/processes/cluster.nf +++ b/src/scanpy/processes/cluster.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths import groovy.transform.TupleConstructor diff --git a/src/scanpy/processes/dim_reduction.nf b/src/scanpy/processes/dim_reduction.nf index 7ac489f8..6bee40eb 100644 --- a/src/scanpy/processes/dim_reduction.nf +++ b/src/scanpy/processes/dim_reduction.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths import groovy.transform.TupleConstructor diff --git a/src/scanpy/processes/feature_selection.nf b/src/scanpy/processes/feature_selection.nf index f3c074ea..8124bb0a 100644 --- a/src/scanpy/processes/feature_selection.nf +++ b/src/scanpy/processes/feature_selection.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/scanpy/processes/filter.nf b/src/scanpy/processes/filter.nf index ba0263e3..dffdf9b2 100644 --- a/src/scanpy/processes/filter.nf +++ b/src/scanpy/processes/filter.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/scanpy/processes/marker_genes.nf b/src/scanpy/processes/marker_genes.nf index 03a6f196..da900fa8 100644 --- a/src/scanpy/processes/marker_genes.nf +++ b/src/scanpy/processes/marker_genes.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/scanpy/processes/neighborhood_graph.nf b/src/scanpy/processes/neighborhood_graph.nf index c085acbe..3c36b3b4 100644 --- a/src/scanpy/processes/neighborhood_graph.nf +++ b/src/scanpy/processes/neighborhood_graph.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths import groovy.transform.TupleConstructor diff --git a/src/scanpy/processes/regress_out.nf b/src/scanpy/processes/regress_out.nf index 244298b7..93e6d3f9 100644 --- a/src/scanpy/processes/regress_out.nf +++ b/src/scanpy/processes/regress_out.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scanpy/bin/" : "" diff --git a/src/scanpy/processes/reports.nf b/src/scanpy/processes/reports.nf index 6fd62827..2a731722 100644 --- a/src/scanpy/processes/reports.nf +++ b/src/scanpy/processes/reports.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import static groovy.json.JsonOutput.* import org.yaml.snakeyaml.Yaml diff --git a/src/scanpy/processes/transform.nf b/src/scanpy/processes/transform.nf index 1d844cd1..7b1017e1 100644 --- a/src/scanpy/processes/transform.nf +++ b/src/scanpy/processes/transform.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/scanpy/workflows/bec_bbknn.nf b/src/scanpy/workflows/bec_bbknn.nf index 3fed0565..f37ab71e 100644 --- a/src/scanpy/workflows/bec_bbknn.nf +++ b/src/scanpy/workflows/bec_bbknn.nf @@ -5,7 +5,7 @@ * - batch effect correction using python package bbknn (Park et al. (2018), Fast Batch Alignment of Single Cell Transcriptomes Unifies Multiple Mouse Cell Atlases into an Integrated Landscape) */ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //////////////////////////////////////////////////////// // Import sub-workflows/processes from the utils module: diff --git a/src/scanpy/workflows/bec_mnncorrect.nf b/src/scanpy/workflows/bec_mnncorrect.nf index d4d38cee..5dd8161d 100644 --- a/src/scanpy/workflows/bec_mnncorrect.nf +++ b/src/scanpy/workflows/bec_mnncorrect.nf @@ -3,7 +3,7 @@ * - batch effect correction using python package mnnpy (fast and python version of mnnCorrect (Haghverdi et al, 2018) */ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //////////////////////////////////////////////////////// // Import sub-workflows/processes from the utils module: diff --git a/src/scanpy/workflows/cluster_identification.nf b/src/scanpy/workflows/cluster_identification.nf index c75d820b..62563549 100644 --- a/src/scanpy/workflows/cluster_identification.nf +++ b/src/scanpy/workflows/cluster_identification.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/scanpy/workflows/combine_reports.nf b/src/scanpy/workflows/combine_reports.nf index 155a94c5..45c2c54c 100644 --- a/src/scanpy/workflows/combine_reports.nf +++ b/src/scanpy/workflows/combine_reports.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 include { clean; diff --git a/src/scanpy/workflows/create_report.nf b/src/scanpy/workflows/create_report.nf index 1943d0cb..8ff0f391 100644 --- a/src/scanpy/workflows/create_report.nf +++ b/src/scanpy/workflows/create_report.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/scanpy/workflows/dim_reduction.nf b/src/scanpy/workflows/dim_reduction.nf index 7179e32e..e9d3a1a3 100644 --- a/src/scanpy/workflows/dim_reduction.nf +++ b/src/scanpy/workflows/dim_reduction.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/scanpy/workflows/dim_reduction_pca.nf b/src/scanpy/workflows/dim_reduction_pca.nf index b9793dbf..27a615dd 100644 --- a/src/scanpy/workflows/dim_reduction_pca.nf +++ b/src/scanpy/workflows/dim_reduction_pca.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/scanpy/workflows/hvg_selection.nf b/src/scanpy/workflows/hvg_selection.nf index 0d91d8cd..6381b91a 100644 --- a/src/scanpy/workflows/hvg_selection.nf +++ b/src/scanpy/workflows/hvg_selection.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/scanpy/workflows/neighborhood_graph.nf b/src/scanpy/workflows/neighborhood_graph.nf index b2c4735f..37a1299e 100644 --- a/src/scanpy/workflows/neighborhood_graph.nf +++ b/src/scanpy/workflows/neighborhood_graph.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/scanpy/workflows/normalize_transform.nf b/src/scanpy/workflows/normalize_transform.nf index e1e4ad7c..dc1e62a6 100644 --- a/src/scanpy/workflows/normalize_transform.nf +++ b/src/scanpy/workflows/normalize_transform.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/scanpy/workflows/qc_filter.nf b/src/scanpy/workflows/qc_filter.nf index 20e93495..b3c07494 100644 --- a/src/scanpy/workflows/qc_filter.nf +++ b/src/scanpy/workflows/qc_filter.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/scanpy/workflows/single_sample.nf b/src/scanpy/workflows/single_sample.nf index 59eefd53..2de848cb 100644 --- a/src/scanpy/workflows/single_sample.nf +++ b/src/scanpy/workflows/single_sample.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import static groovy.json.JsonOutput.* diff --git a/src/scenic/main.nf b/src/scenic/main.nf index 22763a8a..34424537 100644 --- a/src/scenic/main.nf +++ b/src/scenic/main.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 include { resolveParams; diff --git a/src/scenic/main.test.nf b/src/scenic/main.test.nf index 80915828..9ceef3d2 100644 --- a/src/scenic/main.test.nf +++ b/src/scenic/main.test.nf @@ -40,7 +40,7 @@ // nextflow -C conf/multi_runs.config,conf/test.config run main.test.nf --test SAVE_SCENIC_MULTI_RUNS_TO_LOOM -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 /////////////////////////////////////////// // Define the parameters for all processes diff --git a/src/scenic/processes/add_correlation.nf b/src/scenic/processes/add_correlation.nf index ae3b1abe..a857f712 100644 --- a/src/scenic/processes/add_correlation.nf +++ b/src/scenic/processes/add_correlation.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 // binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/arboreto_with_multiprocessing.nf b/src/scenic/processes/arboreto_with_multiprocessing.nf index 2f3fd059..747ba1f1 100644 --- a/src/scenic/processes/arboreto_with_multiprocessing.nf +++ b/src/scenic/processes/arboreto_with_multiprocessing.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/aucell.nf b/src/scenic/processes/aucell.nf index d0fcdd5d..f52c6cbf 100644 --- a/src/scenic/processes/aucell.nf +++ b/src/scenic/processes/aucell.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/cistarget.nf b/src/scenic/processes/cistarget.nf index db6cd33b..6621c4a0 100644 --- a/src/scenic/processes/cistarget.nf +++ b/src/scenic/processes/cistarget.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/loomHandler.nf b/src/scenic/processes/loomHandler.nf index 458790d8..cebf52c2 100644 --- a/src/scenic/processes/loomHandler.nf +++ b/src/scenic/processes/loomHandler.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/multiruns/aggregateFeatures.nf b/src/scenic/processes/multiruns/aggregateFeatures.nf index f574a556..a7da8ece 100644 --- a/src/scenic/processes/multiruns/aggregateFeatures.nf +++ b/src/scenic/processes/multiruns/aggregateFeatures.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/multiruns/aggregateRegulons.nf b/src/scenic/processes/multiruns/aggregateRegulons.nf index 557eec4a..da1546a2 100644 --- a/src/scenic/processes/multiruns/aggregateRegulons.nf +++ b/src/scenic/processes/multiruns/aggregateRegulons.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/multiruns/aucellFromFolder.nf b/src/scenic/processes/multiruns/aucellFromFolder.nf index fba8e0c9..2a3c88f9 100644 --- a/src/scenic/processes/multiruns/aucellFromFolder.nf +++ b/src/scenic/processes/multiruns/aucellFromFolder.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/multiruns/convertMotifsToRegulons.nf b/src/scenic/processes/multiruns/convertMotifsToRegulons.nf index fc2122a6..f735446f 100644 --- a/src/scenic/processes/multiruns/convertMotifsToRegulons.nf +++ b/src/scenic/processes/multiruns/convertMotifsToRegulons.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/multiruns/saveToLoom.nf b/src/scenic/processes/multiruns/saveToLoom.nf index b0e5da50..d2d8b6a7 100644 --- a/src/scenic/processes/multiruns/saveToLoom.nf +++ b/src/scenic/processes/multiruns/saveToLoom.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/processes/reports.nf b/src/scenic/processes/reports.nf index 2fcbb5ae..b8552dc0 100644 --- a/src/scenic/processes/reports.nf +++ b/src/scenic/processes/reports.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/scenic/bin/" : "" diff --git a/src/scenic/workflows/aggregateMultiRuns.nf b/src/scenic/workflows/aggregateMultiRuns.nf index f3ff0ab7..657b0950 100644 --- a/src/scenic/workflows/aggregateMultiRuns.nf +++ b/src/scenic/workflows/aggregateMultiRuns.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/scrublet/processes/doublet_detection.nf b/src/scrublet/processes/doublet_detection.nf index 5cd2f33a..e43c12a0 100644 --- a/src/scrublet/processes/doublet_detection.nf +++ b/src/scrublet/processes/doublet_detection.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths import groovy.transform.TupleConstructor diff --git a/src/scrublet/processes/reports.nf b/src/scrublet/processes/reports.nf index 180e1882..86c96b5d 100644 --- a/src/scrublet/processes/reports.nf +++ b/src/scrublet/processes/reports.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 process SC__SCRUBLET__DOUBLET_DETECTION_REPORT { diff --git a/src/scrublet/workflows/doublet_removal.nf b/src/scrublet/workflows/doublet_removal.nf index d76cca4a..eb50af71 100644 --- a/src/scrublet/workflows/doublet_removal.nf +++ b/src/scrublet/workflows/doublet_removal.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/singlecelltoolkit/processes/barcode_correction.nf b/src/singlecelltoolkit/processes/barcode_correction.nf index bd3122c6..4fe9d9ac 100644 --- a/src/singlecelltoolkit/processes/barcode_correction.nf +++ b/src/singlecelltoolkit/processes/barcode_correction.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolkit/bin/" : "" diff --git a/src/singlecelltoolkit/processes/debarcode_10x_scatac_fastqs.nf b/src/singlecelltoolkit/processes/debarcode_10x_scatac_fastqs.nf index 3d6ad361..0567aea1 100644 --- a/src/singlecelltoolkit/processes/debarcode_10x_scatac_fastqs.nf +++ b/src/singlecelltoolkit/processes/debarcode_10x_scatac_fastqs.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolkit/bin/" : "" diff --git a/src/sinto/main.nf b/src/sinto/main.nf index 715c7ab2..ccb2e4f7 100644 --- a/src/sinto/main.nf +++ b/src/sinto/main.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // Import sub-workflows from the modules: diff --git a/src/sinto/processes/fragments.nf b/src/sinto/processes/fragments.nf index b9fdbff4..a23c6b80 100644 --- a/src/sinto/processes/fragments.nf +++ b/src/sinto/processes/fragments.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/soupx/main.nf b/src/soupx/main.nf index a615618d..d46da119 100644 --- a/src/soupx/main.nf +++ b/src/soupx/main.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 // Should be set in case this pipeline is run with other pipelines (e.g.: single_sample) diff --git a/src/soupx/main.test.nf b/src/soupx/main.test.nf index 8d627f87..bf06320f 100644 --- a/src/soupx/main.test.nf +++ b/src/soupx/main.test.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 include { INIT; diff --git a/src/soupx/processes/process1.nf b/src/soupx/processes/process1.nf index b62be9dd..a572755f 100644 --- a/src/soupx/processes/process1.nf +++ b/src/soupx/processes/process1.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : "" diff --git a/src/soupx/processes/runSoupX.nf b/src/soupx/processes/runSoupX.nf index cb2c84f9..11553a2f 100644 --- a/src/soupx/processes/runSoupX.nf +++ b/src/soupx/processes/runSoupX.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/soupx/workflows/soupX.nf b/src/soupx/workflows/soupX.nf index 7d771825..2c50b617 100644 --- a/src/soupx/workflows/soupX.nf +++ b/src/soupx/workflows/soupX.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/sratoolkit/processes/downloadFastQ.nf b/src/sratoolkit/processes/downloadFastQ.nf index 297b69ca..4768e388 100644 --- a/src/sratoolkit/processes/downloadFastQ.nf +++ b/src/sratoolkit/processes/downloadFastQ.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 if(!params.containsKey("test")) { binDir = "${workflow.projectDir}/src/sratoolkit/bin/" diff --git a/src/star/main.nf b/src/star/main.nf index 93402f0a..eafd9381 100644 --- a/src/star/main.nf +++ b/src/star/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/star/processes/build_genome.nf b/src/star/processes/build_genome.nf index e51b187e..273ee58b 100644 --- a/src/star/processes/build_genome.nf +++ b/src/star/processes/build_genome.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 process SC__STAR__BUILD_INDEX { diff --git a/src/star/processes/load_genome.nf b/src/star/processes/load_genome.nf index a25aeb67..adc794a7 100644 --- a/src/star/processes/load_genome.nf +++ b/src/star/processes/load_genome.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 process SC__STAR__LOAD_GENOME { diff --git a/src/star/processes/map_count.nf b/src/star/processes/map_count.nf index fd0e9505..1fac3f90 100644 --- a/src/star/processes/map_count.nf +++ b/src/star/processes/map_count.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 process SC__STAR__MAP_COUNT { diff --git a/src/star/processes/solo_map_count.nf b/src/star/processes/solo_map_count.nf index 0e26c225..b839329e 100644 --- a/src/star/processes/solo_map_count.nf +++ b/src/star/processes/solo_map_count.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 process SC__STAR__SOLO_MAP_COUNT { container params.sc.star.container diff --git a/src/star/processes/unload_genome.nf b/src/star/processes/unload_genome.nf index 932286f7..77d5a429 100644 --- a/src/star/processes/unload_genome.nf +++ b/src/star/processes/unload_genome.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 process SC__STAR__UNLOAD_GENOME { diff --git a/src/trimgalore/processes/trim.nf b/src/trimgalore/processes/trim.nf index 3a02e8de..02e9a9f9 100644 --- a/src/trimgalore/processes/trim.nf +++ b/src/trimgalore/processes/trim.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/utils/main.test.nf b/src/utils/main.test.nf index c99b294b..92159c70 100644 --- a/src/utils/main.test.nf +++ b/src/utils/main.test.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 include { INIT; diff --git a/src/utils/processes/gtf.nf b/src/utils/processes/gtf.nf index 11c111e5..0e568550 100644 --- a/src/utils/processes/gtf.nf +++ b/src/utils/processes/gtf.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 process FORMAT_GTF { diff --git a/src/utils/processes/h5adAnnotate.nf b/src/utils/processes/h5adAnnotate.nf index df6c9f44..bdab3c1b 100644 --- a/src/utils/processes/h5adAnnotate.nf +++ b/src/utils/processes/h5adAnnotate.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/utils/processes/h5adExtractMetadata.nf b/src/utils/processes/h5adExtractMetadata.nf index 23f9a0e6..f25d3430 100644 --- a/src/utils/processes/h5adExtractMetadata.nf +++ b/src/utils/processes/h5adExtractMetadata.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/utils/processes/h5adMerge.nf b/src/utils/processes/h5adMerge.nf index 25dbafba..43acb06b 100644 --- a/src/utils/processes/h5adMerge.nf +++ b/src/utils/processes/h5adMerge.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/utils/processes/h5adSubset.nf b/src/utils/processes/h5adSubset.nf index 61290f74..30f41f60 100644 --- a/src/utils/processes/h5adSubset.nf +++ b/src/utils/processes/h5adSubset.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/utils/processes/h5adToLoom.nf b/src/utils/processes/h5adToLoom.nf index 8c4c90b7..d1d6cf5c 100644 --- a/src/utils/processes/h5adToLoom.nf +++ b/src/utils/processes/h5adToLoom.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/utils/processes/h5adUpdate.nf b/src/utils/processes/h5adUpdate.nf index 2b308426..5cb7506a 100644 --- a/src/utils/processes/h5adUpdate.nf +++ b/src/utils/processes/h5adUpdate.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths import static groovy.json.JsonOutput.* diff --git a/src/utils/processes/h5adUpdateMetadata.nf b/src/utils/processes/h5adUpdateMetadata.nf index 18e98882..fb829160 100644 --- a/src/utils/processes/h5adUpdateMetadata.nf +++ b/src/utils/processes/h5adUpdateMetadata.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths diff --git a/src/utils/processes/reports.nf b/src/utils/processes/reports.nf index d23970bf..3779f98c 100644 --- a/src/utils/processes/reports.nf +++ b/src/utils/processes/reports.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import static groovy.json.JsonOutput.* diff --git a/src/utils/processes/sra.nf b/src/utils/processes/sra.nf index 7d3f682c..2fc2afc5 100644 --- a/src/utils/processes/sra.nf +++ b/src/utils/processes/sra.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Files import java.nio.file.Paths diff --git a/src/utils/processes/utils.nf b/src/utils/processes/utils.nf index 8388e204..b3647ed9 100644 --- a/src/utils/processes/utils.nf +++ b/src/utils/processes/utils.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Paths import nextflow.config.ConfigParser diff --git a/src/utils/workflows/annotateByCellMetadata.nf b/src/utils/workflows/annotateByCellMetadata.nf index 887a662c..3fceb5e7 100644 --- a/src/utils/workflows/annotateByCellMetadata.nf +++ b/src/utils/workflows/annotateByCellMetadata.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // Process imports: diff --git a/src/utils/workflows/downloadFromSRA.nf b/src/utils/workflows/downloadFromSRA.nf index 178a1e72..e94ea27e 100644 --- a/src/utils/workflows/downloadFromSRA.nf +++ b/src/utils/workflows/downloadFromSRA.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import java.nio.file.Files import java.nio.file.Paths diff --git a/src/utils/workflows/fileConverter.nf b/src/utils/workflows/fileConverter.nf index 602a7ff7..7fd55fd2 100644 --- a/src/utils/workflows/fileConverter.nf +++ b/src/utils/workflows/fileConverter.nf @@ -1,6 +1,6 @@ import nextflow.util.ArrayBag -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/utils/workflows/filterAnnotateClean.nf b/src/utils/workflows/filterAnnotateClean.nf index 74a57623..aca918cf 100644 --- a/src/utils/workflows/filterAnnotateClean.nf +++ b/src/utils/workflows/filterAnnotateClean.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // Process imports: diff --git a/src/utils/workflows/filterByCellMetadata.nf b/src/utils/workflows/filterByCellMetadata.nf index 158ce902..4e6b26e6 100644 --- a/src/utils/workflows/filterByCellMetadata.nf +++ b/src/utils/workflows/filterByCellMetadata.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // Process imports: diff --git a/src/utils/workflows/finalize.nf b/src/utils/workflows/finalize.nf index 041964ad..a30a84d8 100644 --- a/src/utils/workflows/finalize.nf +++ b/src/utils/workflows/finalize.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 include { SC__H5AD_TO_FILTERED_LOOM diff --git a/src/utils/workflows/updateFeatureNomenclature.nf b/src/utils/workflows/updateFeatureNomenclature.nf index 62f11986..3e9c4df4 100644 --- a/src/utils/workflows/updateFeatureNomenclature.nf +++ b/src/utils/workflows/updateFeatureNomenclature.nf @@ -4,7 +4,7 @@ * */ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/src/utils/workflows/utils.nf b/src/utils/workflows/utils.nf index 790ec73f..392afdf9 100644 --- a/src/utils/workflows/utils.nf +++ b/src/utils/workflows/utils.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 import static groovy.json.JsonOutput.* diff --git a/workflows/atac/preprocess.nf b/workflows/atac/preprocess.nf index f5e958f9..6d33d919 100644 --- a/workflows/atac/preprocess.nf +++ b/workflows/atac/preprocess.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/workflows/atac/qc_filtering.nf b/workflows/atac/qc_filtering.nf index 397581fd..5f2358f7 100644 --- a/workflows/atac/qc_filtering.nf +++ b/workflows/atac/qc_filtering.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // process imports: diff --git a/workflows/bbknn.nf b/workflows/bbknn.nf index 1cecb647..816667f8 100644 --- a/workflows/bbknn.nf +++ b/workflows/bbknn.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //////////////////////////////////////////////////////// // Import sub-workflows/processes from the utils module: diff --git a/workflows/harmony.nf b/workflows/harmony.nf index f8a383f0..5743c008 100644 --- a/workflows/harmony.nf +++ b/workflows/harmony.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //////////////////////////////////////////////////////// // Import sub-workflows/processes from the utils module: diff --git a/workflows/mnncorrect.nf b/workflows/mnncorrect.nf index 06e003f8..584621be 100644 --- a/workflows/mnncorrect.nf +++ b/workflows/mnncorrect.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //////////////////////////////////////////////////////// // Import sub-workflows/processes from the utils module: diff --git a/workflows/multi_sample.nf b/workflows/multi_sample.nf index a8ee593f..ff7f5368 100644 --- a/workflows/multi_sample.nf +++ b/workflows/multi_sample.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //////////////////////////////////////////////////////// // Import sub-workflows/processes from the utils module: diff --git a/workflows/nemesh.nf b/workflows/nemesh.nf index a4d5073c..d489e46c 100644 --- a/workflows/nemesh.nf +++ b/workflows/nemesh.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // Define the parameters for current testing proces diff --git a/workflows/single_sample.nf b/workflows/single_sample.nf index ce04497a..1100c25e 100644 --- a/workflows/single_sample.nf +++ b/workflows/single_sample.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 // Utils include { diff --git a/workflows/single_sample_star.nf b/workflows/single_sample_star.nf index 9f95175a..893aba35 100644 --- a/workflows/single_sample_star.nf +++ b/workflows/single_sample_star.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 //////////////////////////////////////////////////////// // Import sub-workflows/processes from the utils module: diff --git a/workflows/star.nf b/workflows/star.nf index 8e07cb68..e4065e5f 100644 --- a/workflows/star.nf +++ b/workflows/star.nf @@ -1,4 +1,4 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 ////////////////////////////////////////////////////// // Define the parameters for current testing proces