From 68fb4f412c2ac9de77452c5b12c9366253a28e59 Mon Sep 17 00:00:00 2001 From: aclum Date: Fri, 4 Oct 2024 11:00:12 -0700 Subject: [PATCH 1/2] Update import-mt.yaml Some updates to import-mt.yaml, not done yet. --- configs/import-mt.yaml | 72 +++++++++++++++++++++--------------------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/configs/import-mt.yaml b/configs/import-mt.yaml index 16788c85..ce116ef3 100644 --- a/configs/import-mt.yaml +++ b/configs/import-mt.yaml @@ -1,20 +1,20 @@ Workflows: - Name: Metatranscriptome Reads QC Import: true - Type: nmdc:ReadQcAnalysisActivity + Type: nmdc:ReadQcAnalysis Git_repo: https://github.com/microbiomedata/metaT_ReadsQC Version: v0.0.7 - Collection: read_qc_analysis_activity_set + Collection: workflow_execution_set/ ActivityRange: ReadQcAnalysisActivity Inputs: - Metagenome Raw Reads Activity: - name: "Read QC Activity for {id}" + name: "Read QC for {id}" input_read_bases: "{outputs.stats.input_read_bases}" input_read_count: "{outputs.stats.input_read_count}" output_read_bases: "{outputs.stats.output_read_bases}" output_read_count: "{outputs.stats.output_read_count}" - type: nmdc:ReadQcAnalysisActivity + type: nmdc:ReadQcAnalysis Outputs: - Filtered Sequencing Reads - QC Statistics @@ -26,7 +26,7 @@ Workflows: Type: nmdc:MetatranscriptomeAssembly Git_repo: https://github.com/microbiomedata/metaT_Assembly Version: v0.0.2 - Collection: metatranscriptome_assembly_set + Collection: workflow_execution_set/ ActivityRange: MetatranscriptomeAssembly Inputs: - Filtered Sequencing Reads @@ -67,16 +67,16 @@ Workflows: - Name: Metatranscriptome Annotation Import: false - Type: nmdc:MetatranscriptomeAnnotationActivity + Type: nmdc:MetatranscriptomeAnnotation Git_repo: https://github.com/microbiomedata/mg_annotation Version: v1.1.4 - Collection: metatranscriptome_annotation_set - ActivityRange: MetatranscriptomeAnnotationActivity + Collection: workflow_execution_set + ActivityRange: MetatranscriptomeAnnotation Inputs: - Assembly Contigs Activity: name: "Metatranscriptome Annotation Analysis Activity for {id}" - type: nmdc:MetatranscriptomeAnnotationActivity + type: nmdc:MetatranscriptomeAnnotation Outputs: - Annotation Amino Acid FASTA - Structural Annotation GFF @@ -130,7 +130,7 @@ Data Objects: name: Raw sequencer read data import_suffix: .[A-Z]+-[A-Z]+.fastq.gz nmdc_suffix: .fastq.gz - input_to: [nmdc:ReadQcAnalysisActivity] + input_to: [nmdc:ReadQcAnalysis] output_of: nmdc:OmicsProcessing mulitple: false action: none @@ -140,7 +140,7 @@ Data Objects: import_suffix: _proteins.faa nmdc_suffix: _proteins.faa input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Contig Mapping File @@ -149,7 +149,7 @@ Data Objects: import_suffix: _contig_names_mapping.tsv nmdc_suffix: _contig_names_mapping.tsv input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Structural Annotation GFF @@ -158,7 +158,7 @@ Data Objects: import_suffix: _structural_annotation.gff nmdc_suffix: _structural_annotation.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Functional Annotation GFF @@ -167,7 +167,7 @@ Data Objects: import_suffix: _functional_annotation.gff nmdc_suffix: _functional_annotation.gff input_to: [nmdc:MetatranscriptomeExpressionAnalysis] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Annotation KEGG Orthology @@ -176,7 +176,7 @@ Data Objects: import_suffix: _ko.tsv nmdc_suffix: _ko.tsv input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Annotation Enzyme Commission @@ -185,7 +185,7 @@ Data Objects: import_suffix: _ec.tsv nmdc_suffix: _ec.tsv input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type Scaffold Lineage tsv @@ -194,7 +194,7 @@ Data Objects: import_suffix: _scaffold_lineage.tsv nmdc_suffix: _scaffold_lineage.tsv input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false - data_object_type: Clusters of Orthologous Groups (COG) Annotation GFF description: COGs for {id} @@ -202,7 +202,7 @@ Data Objects: import_suffix: _cog.gff nmdc_suffix: _cog.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Pfam Annotation GFF @@ -211,7 +211,7 @@ Data Objects: import_suffix: _pfam.gff nmdc_suffix: _pfam.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: TIGRFam Annotation GFF @@ -220,7 +220,7 @@ Data Objects: import_suffix: _tigrfam.gff nmdc_suffix: _tigrfam.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: SMART Annotation GFF @@ -229,7 +229,7 @@ Data Objects: import_suffix: _smart.gff nmdc_suffix: _smart.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: SUPERFam Annotation GFF @@ -238,7 +238,7 @@ Data Objects: import_suffix: _supfam.gff nmdc_suffix: _supfam.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: CATH FunFams (Functional Families) Annotation GFF @@ -247,7 +247,7 @@ Data Objects: import_suffix: _cath_funfam.gff nmdc_suffix: _cath_funfam.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: CRT Annotation GFF @@ -256,7 +256,7 @@ Data Objects: import_suffix: _crt.gff nmdc_suffix: _crt.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Genemark Annotation GFF @@ -265,7 +265,7 @@ Data Objects: import_suffix: _genemark.gff nmdc_suffix: _genemark.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Prodigal Annotation GFF @@ -274,7 +274,7 @@ Data Objects: import_suffix: _prodigal.gff nmdc_suffix: _prodigal.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: TRNA Annotation GFF @@ -283,7 +283,7 @@ Data Objects: import_suffix: _trna.gff nmdc_suffix: _trna.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: RFAM Annotation GFF @@ -292,7 +292,7 @@ Data Objects: import_suffix: _rfam.gff nmdc_suffix: _rfam.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: KO_EC Annotation GFF @@ -301,7 +301,7 @@ Data Objects: import_suffix: _ko_ec.gff nmdc_suffix: _ko_ec.gff input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Product Names @@ -310,7 +310,7 @@ Data Objects: import_suffix: _product_names.tsv nmdc_suffix: _product_names.tsv input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Gene Phylogeny tsv @@ -319,7 +319,7 @@ Data Objects: import_suffix: _gene_phylogeny.tsv nmdc_suffix: _gene_phylogeny.tsv input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Crispr Terms @@ -328,7 +328,7 @@ Data Objects: import_suffix: _crt.crisprs nmdc_suffix: _crt.crisprs input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Annotation Statistics @@ -337,7 +337,7 @@ Data Objects: import_suffix: _stats.tsv nmdc_suffix: _stats.tsv input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Annotation Info File @@ -346,7 +346,7 @@ Data Objects: import_suffix: _imgap.info nmdc_suffix: _imgap.info input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false action: rename - data_object_type: Assembly Contigs @@ -354,7 +354,7 @@ Data Objects: import_suffix: _contigs.fna nmdc_suffix: _renamed_contigs.fna input_to: [] - output_of: nmdc:MetatranscriptomeAnnotationActivity + output_of: nmdc:MetatranscriptomeAnnotation mulitple: false - data_object_type: Filtered Sequencing Reads description: Reads QC for {id} @@ -397,7 +397,7 @@ Data Objects: name: Final assembly contigs fasta import_suffix: assembly.contigs.fasta nmdc_suffix: _contigs.fna - input_to: [nmdc:MetatranscriptomeAnnotationActivity] + input_to: [nmdc:MetatranscriptomeAnnotation] output_of: nmdc:MetatranscriptomeAssembly mulitple: false action: rename From b1f8a823f8524257c1e42fb2e824207d3e5f3aa2 Mon Sep 17 00:00:00 2001 From: aclum Date: Fri, 4 Oct 2024 12:32:36 -0700 Subject: [PATCH 2/2] Update import-mt.yaml --- configs/import-mt.yaml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/configs/import-mt.yaml b/configs/import-mt.yaml index ce116ef3..1d3eedba 100644 --- a/configs/import-mt.yaml +++ b/configs/import-mt.yaml @@ -4,11 +4,11 @@ Workflows: Type: nmdc:ReadQcAnalysis Git_repo: https://github.com/microbiomedata/metaT_ReadsQC Version: v0.0.7 - Collection: workflow_execution_set/ - ActivityRange: ReadQcAnalysisActivity + Collection: workflow_execution_set + WorkflowExecutionRange: ReadQcAnalysis Inputs: - Metagenome Raw Reads - Activity: + Workflow_Execution: name: "Read QC for {id}" input_read_bases: "{outputs.stats.input_read_bases}" input_read_count: "{outputs.stats.input_read_count}" @@ -26,12 +26,12 @@ Workflows: Type: nmdc:MetatranscriptomeAssembly Git_repo: https://github.com/microbiomedata/metaT_Assembly Version: v0.0.2 - Collection: workflow_execution_set/ - ActivityRange: MetatranscriptomeAssembly + Collection: workflow_execution_set + WorkflowExecutionRange: MetatranscriptomeAssembly Inputs: - Filtered Sequencing Reads - Activity: - name: "Metagenome Assembly Activity for {id}" + Workflow_Execution: + name: "Metagenome Assembly for {id}" type: nmdc:MetatranscriptomeAssembly asm_score: "{outputs.stats.asm_score}" contig_bp: "{outputs.stats.contig_bp}" @@ -71,11 +71,11 @@ Workflows: Git_repo: https://github.com/microbiomedata/mg_annotation Version: v1.1.4 Collection: workflow_execution_set - ActivityRange: MetatranscriptomeAnnotation + WorkflowExecutionRange: MetatranscriptomeAnnotation Inputs: - Assembly Contigs - Activity: - name: "Metatranscriptome Annotation Analysis Activity for {id}" + Workflow_Execution: + name: "Metatranscriptome Annotation Analysis for {id}" type: nmdc:MetatranscriptomeAnnotation Outputs: - Annotation Amino Acid FASTA @@ -111,12 +111,12 @@ Workflows: Git_repo: https://github.com/microbiomedata/metaT_ReadCounts Version: v0.0.5 Collection: metatranscriptome_expression_analysis_set - ActivityRange: MetatranscriptomeExpressionAnalysis + WorkflowExecutionRange: MetatranscriptomeExpressionAnalysis Inputs: - Functional Annotation GFF - Contig Mapping File - Assembly Coverage BAM - Activity: + Workflow_Execution: name: "Metatranscriptome Expression Analysis for {id}" type: nmdc:MetatranscriptomeExpressionAnalysis Outputs: @@ -131,7 +131,7 @@ Data Objects: import_suffix: .[A-Z]+-[A-Z]+.fastq.gz nmdc_suffix: .fastq.gz input_to: [nmdc:ReadQcAnalysis] - output_of: nmdc:OmicsProcessing + output_of: nmdc:NucleotideSequencing mulitple: false action: none - data_object_type: Annotation Amino Acid FASTA @@ -362,7 +362,7 @@ Data Objects: import_suffix: filter-MTF.fastq.gz nmdc_suffix: _filtered.fastq.gz input_to: [nmdc:MetatranscriptomeAssembly] - output_of: nmdc:ReadQcAnalysisActivity + output_of: nmdc:ReadQcAnalysis mulitple: false action: rename - data_object_type: rRNA Filtered Sequencing Reads @@ -371,7 +371,7 @@ Data Objects: import_suffix: .rRNA.fastq.gz nmdc_suffix: _rRNA.fastq.gz input_to: [] - output_of: nmdc:ReadQcAnalysisActivity + output_of: nmdc:ReadQcAnalysis mulitple: false action: rename - data_object_type: QC Statistics @@ -380,7 +380,7 @@ Data Objects: import_suffix: .filtered-report.txt nmdc_suffix: _filterStats.txt input_to: [] - output_of: nmdc:ReadQcAnalysisActivity + output_of: nmdc:ReadQcAnalysis mulitple: false action: rename - data_object_type: Read Filtering Info File @@ -389,7 +389,7 @@ Data Objects: import_suffix: .filter_cmd-MTF.sh nmdc_suffix: _readsQC.info input_to: [] - output_of: nmdc:ReadQcAnalysisActivity + output_of: nmdc:ReadQcAnalysis mulitple: false action: rename - data_object_type: Assembly Contigs