Merge pull request #140 from broadinstitute/dp-trs-build

dockstore.yml fix

.dockstore.yml

@@ -2,226 +2,226 @@ version: 1.2
 workflows:
  - name: align_and_count_multiple_report
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/align_and_count_multiple_report.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/align_and_count_multiple_report.wdl
    testParameterFiles:
     - empty.json
  - name: align_and_count
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/align_and_count.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/align_and_count.wdl
    testParameterFiles:
     - empty.json
  - name: align_and_plot
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/align_and_plot.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/align_and_plot.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-align_and_plot-local.json
+    - /test/input/WDL/test_inputs-align_and_plot-local.json
  - name: assemble_denovo
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/assemble_denovo.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/assemble_denovo.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-assemble_denovo-local.json
+    - /test/input/WDL/test_inputs-assemble_denovo-local.json
  - name: assemble_refbased
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/assemble_refbased.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/assemble_refbased.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-assemble_refbased-local.json
+    - /test/input/WDL/test_inputs-assemble_refbased-local.json
  - name: augur_from_assemblies
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/augur_from_assemblies.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/augur_from_assemblies.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-augur_from_assemblies-local.json
+    - /test/input/WDL/test_inputs-augur_from_assemblies-local.json
  - name: augur_from_beast_mcc
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/augur_from_beast_mcc.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/augur_from_beast_mcc.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-augur_from_beast_mcc-local.json
+    - /test/input/WDL/test_inputs-augur_from_beast_mcc-local.json
  - name: augur_from_msa
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/augur_from_msa.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/augur_from_msa.wdl
    testParameterFiles:
     - empty.json
  - name: augur_from_newick
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/augur_from_newick.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/augur_from_newick.wdl
    testParameterFiles:
     - empty.json
  - name: bams_multiqc
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/bams_multiqc.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/bams_multiqc.wdl
    testParameterFiles:
     - empty.json
  - name: beast_gpu
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/beast_gpu.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/beast_gpu.wdl
    testParameterFiles:
     - empty.json
  - name: classify_kaiju
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/classify_kaiju.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/classify_kaiju.wdl
    testParameterFiles:
     - empty.json
  - name: classify_kraken2
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/classify_kraken2.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/classify_kraken2.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-classify_kraken2-local.json
+    - /test/input/WDL/test_inputs-classify_kraken2-local.json
  - name: classify_krakenuniq
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/classify_krakenuniq.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/classify_krakenuniq.wdl
    testParameterFiles:
     - empty.json
  - name: classify_multi
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/classify_multi.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/classify_multi.wdl
    testParameterFiles:
     - empty.json
  - name: classify_single
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/classify_single.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/classify_single.wdl
    testParameterFiles:
     - empty.json
  - name: contigs
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/contigs.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/contigs.wdl
    testParameterFiles:
     - empty.json
  - name: coverage_table
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/coverage_table.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/coverage_table.wdl
    testParameterFiles:
     - empty.json
  - name: demux_metag
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/demux_metag.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/demux_metag.wdl
    testParameterFiles:
     - empty.json
  - name: demux_only
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/demux_only.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/demux_only.wdl
    testParameterFiles:
     - empty.json
  - name: demux_plus
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/demux_plus.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/demux_plus.wdl
    testParameterFiles:
     - empty.json
  - name: deplete_only
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/deplete_only.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/deplete_only.wdl
    testParameterFiles:
     - empty.json
  - name: diff_genome_sets
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/diff_genome_sets.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/diff_genome_sets.wdl
    testParameterFiles:
     - empty.json
  - name: downsample
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/downsample.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/downsample.wdl
    testParameterFiles:
     - empty.json
  - name: fastq_to_ubam
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/fastq_to_ubam.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/fastq_to_ubam.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-fastq_to_ubam-local.json
+    - /test/input/WDL/test_inputs-fastq_to_ubam-local.json
  - name: fetch_annotations
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/fetch_annotations.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/fetch_annotations.wdl
    testParameterFiles:
     - empty.json
  - name: fetch_sra_to_bam
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/fetch_sra_to_bam.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/fetch_sra_to_bam.wdl
    testParameterFiles:
     - empty.json
  - name: filter_classified_bam_to_taxa
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl
    testParameterFiles:
     - empty.json
  - name: filter_sequences
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/filter_sequences.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/filter_sequences.wdl
    testParameterFiles:
     - empty.json
  - name: genbank
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/genbank.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/genbank.wdl
    testParameterFiles:
-    - test/input/WDL/test_inputs-genbank-local.json
+    - /test/input/WDL/test_inputs-genbank-local.json
  - name: isnvs_merge_to_vcf
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/isnvs_merge_to_vcf.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/isnvs_merge_to_vcf.wdl
    testParameterFiles:
     - empty.json
  - name: isnvs_one_sample
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/isnvs_one_sample.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/isnvs_one_sample.wdl
    testParameterFiles:
     - empty.json
  - name: kraken2_build
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/kraken2_build.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/kraken2_build.wdl
    testParameterFiles:
     - empty.json
  - name: mafft_and_snp
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/mafft_and_snp.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp.wdl
    testParameterFiles:
     - empty.json
  - name: mafft_and_trim
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/mafft_and_trim.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_trim.wdl
    testParameterFiles:
     - empty.json
  - name: mafft
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/mafft.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/mafft.wdl
    testParameterFiles:
     - empty.json
  - name: merge_bams
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/merge_bams.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/merge_bams.wdl
    testParameterFiles:
     - empty.json
  - name: merge_metagenomics
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/merge_metagenomics.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/merge_metagenomics.wdl
    testParameterFiles:
     - empty.json
  - name: merge_tar_chunks
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/merge_tar_chunks.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/merge_tar_chunks.wdl
    testParameterFiles:
     - empty.json
  - name: merge_vcfs_and_annotate
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/merge_vcfs_and_annotate.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs_and_annotate.wdl
    testParameterFiles:
     - empty.json
  - name: merge_vcfs
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/merge_vcfs.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs.wdl
    testParameterFiles:
     - empty.json
  - name: multiqc_only
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/multiqc_only.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/multiqc_only.wdl
    testParameterFiles:
     - empty.json
  - name: scaffold_and_refine
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/scaffold_and_refine.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/scaffold_and_refine.wdl
    testParameterFiles:
     - empty.json
  - name: subsample_by_metadata
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/subsample_by_metadata.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata.wdl
    testParameterFiles:
     - empty.json
  - name: trimal
    subclass: WDL
-   primaryDescriptorPath: pipes/WDL/workflows/trimal.wdl
+   primaryDescriptorPath: /pipes/WDL/workflows/trimal.wdl
    testParameterFiles:
     - empty.json