Merge branch 'master' into master

broadinstitute · Nov 3, 2022 · 4b68fe8 · 4b68fe8
2 parents 8362a7a + 039ac18
commit 4b68fe8
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diff --git a/.dockstore.yml b/.dockstore.yml
@@ -278,116 +278,17 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_lineages.wdl
     testParameterFiles:
-  - name: isnvs_merge_to_vcf
-    subclass: 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
-    testParameterFiles:
-      - empty.json
-  - name: kraken2_build
-    subclass: 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
-    testParameterFiles:
-      - empty.json
-  - name: mafft_and_snp_annotated
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp_annotated.wdl
-    testParameterFiles:
-      - empty.json
-  - name: mafft_and_trim
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_trim.wdl
-    testParameterFiles:
-      - empty.json
-  - name: mafft
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/mafft.wdl
-    testParameterFiles:
-      - empty.json
-  - name: merge_bams
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/merge_bams.wdl
-    testParameterFiles:
-      - empty.json
-  - name: merge_metagenomics
-    subclass: 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
-    testParameterFiles:
-      - empty.json
-  - name: merge_vcfs_and_annotate
-    subclass: 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
-    testParameterFiles:
-      - empty.json
-  - name: multiqc_only
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/multiqc_only.wdl
-    testParameterFiles:
-      - empty.json
+    - /test/input/WDL/test_inputs-sarscov2_lineages-local.json
   - name: read_depths
     subclass: WDL
     primaryDescriptorPath: /pipes/WDL/workflows/read_depths.wdl
     testParameterFiles:
       - empty.json
-  - name: sarscov2_batch_relineage
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_batch_relineage.wdl
-    testParameterFiles:
-      - empty.json
-  - name: sarscov2_biosample_load
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_biosample_load.wdl
-    testParameterFiles:
-      - empty.json
-  - name: sarscov2_data_release
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_data_release.wdl
-    testParameterFiles:
-      - empty.json
-  - name: sarscov2_genbank
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank.wdl
-    testParameterFiles:
-      - empty.json
-  - name: sarscov2_genbank_ingest
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank_ingest.wdl
-    testParameterFiles:
-      - empty.json
   - name: sarscov2_gisaid_ingest
     subclass: WDL
     primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_gisaid_ingest.wdl
     testParameterFiles:
       - empty.json
-  - name: sarscov2_illumina_full
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_illumina_full.wdl
-    testParameterFiles:
-      - empty.json
-  - name: sarscov2_lineages
-    subclass: WDL
-    primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_lineages.wdl
-    testParameterFiles:
-    - /test/input/WDL/test_inputs-sarscov2_lineages-local.json
   - name: sarscov2_nextclade_multi
     subclass: WDL
     primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextclade_multi.wdl

diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl
@@ -61,9 +61,9 @@ task nextclade_one_sample {
                 for c in zip(*(l.rstrip().split('\t') for l in inf)):
                     outf.write('\t'.join(c)+'\n')
         CODE
-        grep ^clade transposed.tsv | cut -f 2 | grep -v clade > NEXTCLADE_CLADE
-        grep ^aaSubstitutions transposed.tsv | cut -f 2 | grep -v aaSubstitutions > NEXTCLADE_AASUBS
-        grep ^aaDeletions transposed.tsv | cut -f 2 | grep -v aaDeletions > NEXTCLADE_AADELS
+        grep ^clade\\W transposed.tsv | cut -f 2 | grep -v clade > NEXTCLADE_CLADE
+        grep ^aaSubstitutions\\W transposed.tsv | cut -f 2 | grep -v aaSubstitutions > NEXTCLADE_AASUBS
+        grep ^aaDeletions\\W transposed.tsv | cut -f 2 | grep -v aaDeletions > NEXTCLADE_AADELS
     }
     runtime {
         docker: docker