From 0b11e33307bc12752d83ebbae4fde0acd4dbcba2 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Wed, 14 Feb 2024 10:03:15 -0500 Subject: [PATCH] fix for dockstore updates --- .dockstore.yml | 142 ++++++++++++++++++++++++------------------------- 1 file changed, 71 insertions(+), 71 deletions(-) diff --git a/.dockstore.yml b/.dockstore.yml index be93a4ad5..c359fd887 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -4,12 +4,12 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/align_and_count_multiple_report.wdl testParameterFiles: - - empty.json + - /empty.json - name: align_and_count subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/align_and_count.wdl testParameterFiles: - - empty.json + - /empty.json - name: align_and_plot subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/align_and_plot.wdl @@ -29,7 +29,7 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/augur_export_only.wdl testParameterFiles: - - empty.json + - /empty.json - name: augur_from_assemblies subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/augur_from_assemblies.wdl @@ -44,32 +44,32 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/augur_from_mltree.wdl testParameterFiles: - - empty.json + - /empty.json - name: augur_from_msa subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/augur_from_msa.wdl testParameterFiles: - - empty.json + - /empty.json - name: augur_from_msa_with_subsampler subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/augur_from_msa_with_subsampler.wdl testParameterFiles: - - empty.json + - /empty.json - name: bams_multiqc subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/bams_multiqc.wdl testParameterFiles: - - empty.json + - /empty.json - name: beast_gpu subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/beast_gpu.wdl testParameterFiles: - - empty.json + - /empty.json - name: classify_kaiju subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/classify_kaiju.wdl testParameterFiles: - - empty.json + - /empty.json - name: classify_kraken2 subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/classify_kraken2.wdl @@ -79,57 +79,57 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/classify_krakenuniq.wdl testParameterFiles: - - empty.json + - /empty.json - name: classify_multi subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/classify_multi.wdl testParameterFiles: - - empty.json + - /empty.json - name: classify_single subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/classify_single.wdl testParameterFiles: - - empty.json + - /empty.json - name: contigs subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/contigs.wdl testParameterFiles: - - empty.json + - /empty.json - name: coverage_table subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/coverage_table.wdl testParameterFiles: - - empty.json + - /empty.json - name: demux_metag subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/demux_metag.wdl testParameterFiles: - - empty.json + - /empty.json - name: demux_only subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/demux_only.wdl testParameterFiles: - - empty.json + - /empty.json - name: demux_deplete subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/demux_deplete.wdl testParameterFiles: - - empty.json + - /empty.json - name: demux_deplete_and_table_insert subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/demux_deplete_and_table_insert.wdl testParameterFiles: - - empty.json + - /empty.json - name: demux_plus subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/demux_plus.wdl testParameterFiles: - - empty.json + - /empty.json - name: deplete_only subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/deplete_only.wdl testParameterFiles: - - empty.json + - /empty.json - name: detect_cross_contamination subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/detect_cross_contamination.wdl @@ -138,22 +138,22 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/detect_cross_contamination_precalled_vcfs.wdl testParameterFiles: - - empty.json + - /empty.json - name: diff_genome_sets subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/diff_genome_sets.wdl testParameterFiles: - - empty.json + - /empty.json - name: downsample subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/downsample.wdl testParameterFiles: - - empty.json + - /empty.json - name: dump_gcloud_env_info subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/dump_gcloud_env_info.wdl testParameterFiles: - - empty.json + - /empty.json - name: fastq_to_ubam subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/fastq_to_ubam.wdl @@ -163,22 +163,22 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/fetch_annotations.wdl testParameterFiles: - - empty.json + - /empty.json - name: fetch_sra_to_bam subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/fetch_sra_to_bam.wdl testParameterFiles: - - empty.json + - /empty.json - name: filter_classified_bam_to_taxa subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl testParameterFiles: - - empty.json + - /empty.json - name: filter_sequences subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/filter_sequences.wdl testParameterFiles: - - empty.json + - /empty.json - name: genbank subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/genbank.wdl @@ -188,122 +188,122 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/isnvs_merge_to_vcf.wdl testParameterFiles: - - empty.json + - /empty.json - name: isnvs_lofreq subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/isnvs_lofreq.wdl testParameterFiles: - - empty.json + - /empty.json - name: isnvs_one_sample subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/isnvs_one_sample.wdl testParameterFiles: - - empty.json + - /empty.json - name: kraken2_build subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/kraken2_build.wdl testParameterFiles: - - empty.json + - /empty.json - name: mafft_and_snp subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp.wdl testParameterFiles: - - empty.json + - /empty.json - name: mafft_and_snp_annotated subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp_annotated.wdl testParameterFiles: - - empty.json + - /empty.json - name: mafft_and_trim subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_trim.wdl testParameterFiles: - - empty.json + - /empty.json - name: mafft subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/mafft.wdl testParameterFiles: - - empty.json + - /empty.json - name: merge_bams subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/merge_bams.wdl testParameterFiles: - - empty.json + - /empty.json - name: merge_metagenomics subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/merge_metagenomics.wdl testParameterFiles: - - empty.json + - /empty.json - name: merge_tar_chunks subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/merge_tar_chunks.wdl testParameterFiles: - - empty.json + - /empty.json - name: merge_vcfs_and_annotate subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs_and_annotate.wdl testParameterFiles: - - empty.json + - /empty.json - name: merge_vcfs subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs.wdl testParameterFiles: - - empty.json + - /empty.json - name: metagenomic_denovo subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/metagenomic_denovo.wdl testParameterFiles: - - empty.json + - /empty.json - name: multiqc_only subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/multiqc_only.wdl testParameterFiles: - - empty.json + - /empty.json - name: nextclade_single subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/nextclade_single.wdl testParameterFiles: - - empty.json + - /empty.json - name: populate_library_and_sample_tables_from_flowcell subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/populate_library_and_sample_tables_from_flowcell.wdl testParameterFiles: - - empty.json + - /empty.json - name: reconstruct_from_alignments subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/reconstruct_from_alignments.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_batch_relineage subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_batch_relineage.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_biosample_load subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_biosample_load.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_data_release subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_data_release.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_genbank subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_genbank_ingest subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank_ingest.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_illumina_full subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_illumina_full.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_lineages subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_lineages.wdl @@ -313,96 +313,96 @@ workflows: subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/calc_bam_read_depths.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_gisaid_ingest subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_gisaid_ingest.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_nextclade_multi subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextclade_multi.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_nextstrain subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextstrain.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_nextstrain_aligned_input subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_sequencing_reports subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_sequencing_reports.wdl testParameterFiles: - - empty.json + - /empty.json - name: sarscov2_sra_to_genbank subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_sra_to_genbank.wdl testParameterFiles: - - empty.json + - /empty.json - name: scaffold_and_refine subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/scaffold_and_refine.wdl testParameterFiles: - - empty.json + - /empty.json - name: scaffold_and_refine_multitaxa subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl testParameterFiles: - - empty.json + - /empty.json - name: subsample_by_casecounts subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_casecounts.wdl testParameterFiles: - - empty.json + - /empty.json - name: subsample_by_metadata subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata.wdl testParameterFiles: - - empty.json + - /empty.json - name: subsample_by_metadata_with_focal subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata_with_focal.wdl testParameterFiles: - - empty.json + - /empty.json - name: terra_table_to_tsv subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/terra_table_to_tsv.wdl testParameterFiles: - - empty.json + - /empty.json - name: terra_update_assemblies subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/terra_update_assemblies.wdl testParameterFiles: - - empty.json + - /empty.json - name: trimal subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/trimal.wdl testParameterFiles: - - empty.json + - /empty.json - name: classify_qiime2_multi subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/classify_qiime2_multi.wdl testParameterFiles: - - empty.json + - /empty.json - name: qiime_import_bam subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/bam_to_qiime.wdl testParameterFiles: - - empty.json + - /empty.json - name: create_enterics_qc_viz subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz.wdl testParameterFiles: - - empty.json + - /empty.json - name: create_enterics_qc_viz_general subclass: WDL primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz_general.wdl testParameterFiles: - - empty.json + - /empty.json