From a4c52214e526db5aab90f7003156f3b74b2318ce Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 1 Jun 2023 10:06:59 -0400 Subject: [PATCH 01/16] update actions/checkout v2 -> v3 --- .github/workflows/build.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 81c3d1ecf..9e1bc1dd7 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -34,9 +34,9 @@ jobs: runs-on: ubuntu-20.04 steps: - name: checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 # fetch git tags (tagged releases) because - # actions/checkout@v2 does either a full checkout or a shallow checkout without tags + # actions/checkout@v3 does either a full checkout or a shallow checkout without tags - name: fetch tags run: git fetch --prune --unshallow --tags - name: Programmatic environment setup @@ -87,9 +87,9 @@ jobs: runs-on: ubuntu-20.04 steps: - name: checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 # fetch git tags (tagged releases) because - # actions/checkout@v2 does either a full checkout or a shallow checkout without tags + # actions/checkout@v3 does either a full checkout or a shallow checkout without tags - name: fetch tags run: git fetch --prune --unshallow --tags - name: Programmatic environment setup @@ -137,9 +137,9 @@ jobs: runs-on: ubuntu-20.04 steps: - name: checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 # fetch git tags (tagged releases) because - # actions/checkout@v2 does either a full checkout or a shallow checkout without tags + # actions/checkout@v3 does either a full checkout or a shallow checkout without tags - name: fetch tags run: git fetch --prune --unshallow --tags - name: Programmatic environment setup @@ -182,9 +182,9 @@ jobs: runs-on: ubuntu-20.04 steps: - name: checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 # fetch git tags (tagged releases) because - # actions/checkout@v2 does either a full checkout or a shallow checkout without tags + # actions/checkout@v3 does either a full checkout or a shallow checkout without tags - name: fetch tags run: git fetch --prune --unshallow --tags - name: Programmatic environment setup @@ -230,9 +230,9 @@ jobs: runs-on: ubuntu-20.04 steps: - name: checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 # fetch git tags (tagged releases) because - # actions/checkout@v2 does either a full checkout or a shallow checkout without tags + # actions/checkout@v3 does either a full checkout or a shallow checkout without tags - name: fetch tags run: git fetch --prune --unshallow --tags - name: Programmatic environment setup @@ -289,9 +289,9 @@ jobs: DX_PROJECT: project-F8PQ6380xf5bK0Qk0YPjB17P steps: - name: checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 # fetch git tags (tagged releases) because - # actions/checkout@v2 does either a full checkout or a shallow checkout without tags + # actions/checkout@v3 does either a full checkout or a shallow checkout without tags - name: fetch tags run: git fetch --prune --unshallow --tags - name: Programmatic environment setup From 433176ef89e405eb0c381a8e9fcb33a02cdb84d0 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 1 Jun 2023 10:08:09 -0400 Subject: [PATCH 02/16] update actions/setup-python v2 -> v4 --- .github/workflows/build.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9e1bc1dd7..9bcc07f8a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -66,7 +66,7 @@ jobs: run: | env - name: install python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: '3.8' - name: install system dependencies @@ -165,7 +165,7 @@ jobs: echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV - name: install python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: '3.8' - name: install docs dependencies @@ -258,7 +258,7 @@ jobs: echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV - name: install python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: '3.8' - name: install system dependencies @@ -322,7 +322,7 @@ jobs: echo "${{ github.event.action }}" echo "${{ github.event.pull_request.merged }}" - name: install python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: '3.8' - name: install java From 4d1506fb52bef0d6650b07516f50c2b0742be599 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 1 Jun 2023 10:20:05 -0400 Subject: [PATCH 03/16] update actions/setup-java v2 -> v3 --- .github/workflows/build.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9bcc07f8a..11e271237 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -115,7 +115,7 @@ jobs: echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV - name: install java - uses: actions/setup-java@v2 + uses: actions/setup-java@v3 with: distribution: 'adopt' java-version: '11' @@ -210,7 +210,7 @@ jobs: echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV - name: install java - uses: actions/setup-java@v2 + uses: actions/setup-java@v3 with: distribution: 'adopt' java-version: '11' @@ -326,7 +326,7 @@ jobs: with: python-version: '3.8' - name: install java - uses: actions/setup-java@v2 + uses: actions/setup-java@v3 with: distribution: 'adopt' java-version: '11' From 09999524ee9c3e050b573baac3779b8751f74847 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Fri, 28 Jul 2023 13:17:02 -0400 Subject: [PATCH 04/16] extend beast task and workflow to glob and output *.ops, *.rates, and *.root files extend beast task (and workflow) to glob and output *.ops, *.rates, and *.root files, if present --- pipes/WDL/tasks/tasks_interhost.wdl | 3 +++ pipes/WDL/workflows/beast_gpu.wdl | 3 +++ 2 files changed, 6 insertions(+) diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl index 38f64ad66..14598f19c 100644 --- a/pipes/WDL/tasks/tasks_interhost.wdl +++ b/pipes/WDL/tasks/tasks_interhost.wdl @@ -168,6 +168,9 @@ task beast { output { File beast_log = glob("*.log")[0] Array[File] trees = glob("*.trees") + Array[File] ops = glob("*.ops") + Array[File] rates = glob("*.rates") + Array[File] root = glob("*.root") File beast_stdout = stdout() } diff --git a/pipes/WDL/workflows/beast_gpu.wdl b/pipes/WDL/workflows/beast_gpu.wdl index 10c428ca3..1fef20063 100644 --- a/pipes/WDL/workflows/beast_gpu.wdl +++ b/pipes/WDL/workflows/beast_gpu.wdl @@ -13,6 +13,9 @@ workflow beast_gpu { output { File beast_log = beast.beast_log Array[File] trees = beast.trees + Array[File] ops = beast.ops + Array[File] rates = beast.rates + Array[File] root = beast.root String beast_stdout = beast.beast_stdout } } From 08d60396e6dfd47aac5c5ec598ec725746f150b0 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Tue, 8 Aug 2023 10:26:19 -0400 Subject: [PATCH 05/16] configure sam-dump to pull full (i.e. with quality scores) and not "SRA Lite" data See: https://microbial-bioinfo.slack.com/archives/C2BE1SW91/p1691008950582849 --- pipes/WDL/tasks/tasks_ncbi_tools.wdl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pipes/WDL/tasks/tasks_ncbi_tools.wdl b/pipes/WDL/tasks/tasks_ncbi_tools.wdl index 64d0328db..f91d85a7a 100644 --- a/pipes/WDL/tasks/tasks_ncbi_tools.wdl +++ b/pipes/WDL/tasks/tasks_ncbi_tools.wdl @@ -34,6 +34,11 @@ task Fetch_SRA_to_BAM { SAM_PLATFORM="$PLATFORM" fi + # Pull full quality scores (i.e. not "SRA lite" format) + # See: + # https://www.ncbi.nlm.nih.gov/sra/docs/sra-data-formats/ + vdb-config --simplified-quality-scores no + sam-dump --unaligned --header "~{SRA_ID}" \ | samtools view -bhS - \ > temp.bam From 0d60a78633e4289b9aafa187b5b98d6de414b447 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Thu, 10 Aug 2023 13:42:58 -0400 Subject: [PATCH 06/16] hotfix for bug in output path --- pipes/WDL/tasks/tasks_ncbi.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl index bcd46bc5c..7726266d0 100644 --- a/pipes/WDL/tasks/tasks_ncbi.wdl +++ b/pipes/WDL/tasks/tasks_ncbi.wdl @@ -60,7 +60,7 @@ task download_annotations { >>> output { - File combined_fasta = "~{combined_out_prefix}.fasta" + File combined_fasta = "combined/~{combined_out_prefix}.fasta" Array[File] genomes_fasta = glob("*.fasta") Array[File] features_tbl = glob("*.tbl") String viralngs_version = read_string("VERSION") From 1fd0a483ac1f61d8cd863addf268e1b1a91ec609 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Sep 2023 16:38:07 -0400 Subject: [PATCH 07/16] small tweak to speed input processing and reduce temp file sizes --- pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl b/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl index 9d8410ecc..e6f822985 100644 --- a/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl +++ b/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl @@ -13,7 +13,7 @@ workflow sarscov2_nextstrain_aligned_input { } input { - Array[File]+ aligned_sequences_fasta=["gs://nextstrain-data/files/ncov/open/aligned.fasta.xz"] + Array[File]+ aligned_sequences_fasta=["gs://nextstrain-data/files/ncov/open/aligned.fasta.zst"] Array[File]+ sample_metadata_tsvs=["gs://nextstrain-data/files/ncov/open/metadata.tsv.gz"] String build_name @@ -57,7 +57,7 @@ workflow sarscov2_nextstrain_aligned_input { call utils.zcat { input: infiles = aligned_sequences_fasta, - output_name = "all_samples_combined_assembly.fasta" + output_name = "all_samples_combined_assembly.fasta.xz" } #### merge metadata, compute derived cols From 19caeebcda5962fe2bcdecea872d1dde806791bf Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Sep 2023 16:52:07 -0400 Subject: [PATCH 08/16] bump pangolin --- pipes/WDL/tasks/tasks_sarscov2.wdl | 4 ++-- requirements-modules.txt | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl index 041a6f430..cb9866ec3 100644 --- a/pipes/WDL/tasks/tasks_sarscov2.wdl +++ b/pipes/WDL/tasks/tasks_sarscov2.wdl @@ -10,7 +10,7 @@ task pangolin_one_sample { Float? max_ambig String? analysis_mode Boolean update_dbs_now=false - String docker = "quay.io/staphb/pangolin:4.2-pdata-1.18.1.1" + String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.22" } String basename = basename(genome_fasta, ".fasta") Int disk_size = 50 @@ -93,7 +93,7 @@ task pangolin_many_samples { String? analysis_mode Boolean update_dbs_now=false String basename - String docker = "quay.io/staphb/pangolin:4.2-pdata-1.18.1.1" + String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.22" } Int disk_size = 100 command <<< diff --git a/requirements-modules.txt b/requirements-modules.txt index f2dcc6cd1..b20c89a98 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -7,5 +7,5 @@ broadinstitute/beast-beagle-cuda=1.10.5pre broadinstitute/ncbi-tools=2.10.7.10 nextstrain/base=build-20211012T204409Z andersenlabapps/ivar=1.3.1 -quay.io/staphb/pangolin=4.2-pdata-1.18.1.1 +quay.io/staphb/pangolin=4.3.1-pdata-1.22 nextstrain/nextclade=2.12.0 From 644431a89b502702c1aaf908aade086e0a494da3 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Sep 2023 17:17:13 -0400 Subject: [PATCH 09/16] remove pangolin unit test --- .../WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json | 1 - 1 file changed, 1 deletion(-) delete mode 120000 test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json diff --git a/test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json b/test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json deleted file mode 120000 index 59916f987..000000000 --- a/test/input/WDL/miniwdl-local/test_inputs-sarscov2_lineages-local.json +++ /dev/null @@ -1 +0,0 @@ -../test_inputs-sarscov2_lineages-local.json \ No newline at end of file From 34919eb6e93dea226b22d855ea33d1e5d928f6cd Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Sep 2023 17:38:59 -0400 Subject: [PATCH 10/16] remove genbank test from cromwell unit testing --- .../test_inputs-genbank-local.json | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 test/input/WDL/cromwell-local/test_inputs-genbank-local.json diff --git a/test/input/WDL/cromwell-local/test_inputs-genbank-local.json b/test/input/WDL/cromwell-local/test_inputs-genbank-local.json deleted file mode 100644 index e6af063fe..000000000 --- a/test/input/WDL/cromwell-local/test_inputs-genbank-local.json +++ /dev/null @@ -1,21 +0,0 @@ -{ - "genbank.molType": "cRNA", - "genbank.coverage_table": "test/input/genbank/coverage-ma_mgh.txt", - "genbank.alignments_bams": [], - "genbank.reference_accessions": ["MN908947.3"], - "genbank.sequencingTech": "Illumina NovaSeq", - "genbank.biosample_attributes": "test/input/genbank/sars-cov-2_attributes_updated.txt", - "genbank.prep_genbank.assembly_method": "placeholder assembly software", - "genbank.prep_genbank.assembly_method_version": "5.4.3.2.1", - "genbank.comment": "this is only a test -- DO NOT SUBMIT to NCBI", - "genbank.author_list": "Odia,Ikponmwosa, Ehaine,Philomena, Oguzie,Judith,U. Siddle,Katherine,J. Mehta,Samar, Barnes,Kayla,M. Winnicki,Sarah,M. Brehio,Patrick, Shah,Rickey,R. Chak,Bridget, Yozwiak,Nathan, Amao,Adebayo, Nosamiefan,Iguosadolo, Birren,Bruce,W. Park,Daniel,J. Folarin,Onikepe, Okokhere,Peter, Sabeti,Pardis,C. Happi,Christian,T.", - "genbank.author_sbt_defaults_yaml": "test/input/genbank/default_sbt_values.yaml", - "genbank.author_sbt_j2_template": "test/input/genbank/author_template.sbt.j2", - "genbank.assemblies_fasta": [ - "test/input/MA_MGH_00003.fasta", - "test/input/MA_MGH_00004.fasta", - "test/input/MA_MGH_00005.fasta" - ], - "genbank.email_address": "viral-ngs@broadinstitute.org" -} - From 4cc37b26294af81b1bbf837b064459d22366b936 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Sep 2023 17:59:25 -0400 Subject: [PATCH 11/16] Revert "configure sam-dump to pull full (i.e. with quality scores) and not "SRA Lite" data" Keep in separate PR branch This reverts commit 08d60396e6dfd47aac5c5ec598ec725746f150b0. --- pipes/WDL/tasks/tasks_ncbi_tools.wdl | 5 ----- 1 file changed, 5 deletions(-) diff --git a/pipes/WDL/tasks/tasks_ncbi_tools.wdl b/pipes/WDL/tasks/tasks_ncbi_tools.wdl index f91d85a7a..64d0328db 100644 --- a/pipes/WDL/tasks/tasks_ncbi_tools.wdl +++ b/pipes/WDL/tasks/tasks_ncbi_tools.wdl @@ -34,11 +34,6 @@ task Fetch_SRA_to_BAM { SAM_PLATFORM="$PLATFORM" fi - # Pull full quality scores (i.e. not "SRA lite" format) - # See: - # https://www.ncbi.nlm.nih.gov/sra/docs/sra-data-formats/ - vdb-config --simplified-quality-scores no - sam-dump --unaligned --header "~{SRA_ID}" \ | samtools view -bhS - \ > temp.bam From 10ab182feef613354c5ad619266c7b772bc76717 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Sat, 9 Sep 2023 09:22:36 -0400 Subject: [PATCH 12/16] skip qiime workflows for dnax --- pipes/WDL/workflows/bam_to_qiime.wdl | 2 ++ pipes/WDL/workflows/classify_qiime2_multi.wdl | 2 ++ 2 files changed, 4 insertions(+) diff --git a/pipes/WDL/workflows/bam_to_qiime.wdl b/pipes/WDL/workflows/bam_to_qiime.wdl index 650925c1b..b7da1f9a3 100644 --- a/pipes/WDL/workflows/bam_to_qiime.wdl +++ b/pipes/WDL/workflows/bam_to_qiime.wdl @@ -1,5 +1,7 @@ version 1.0 +#DX_SKIP_WORKFLOW + import "../tasks/tasks_16S_amplicon.wdl" as infile workflow qiime_import_bam { diff --git a/pipes/WDL/workflows/classify_qiime2_multi.wdl b/pipes/WDL/workflows/classify_qiime2_multi.wdl index 281f5b0c0..90bbf70fd 100755 --- a/pipes/WDL/workflows/classify_qiime2_multi.wdl +++ b/pipes/WDL/workflows/classify_qiime2_multi.wdl @@ -1,5 +1,7 @@ version 1.0 +#DX_SKIP_WORKFLOW + import "../tasks/tasks_16S_amplicon.wdl" as qiime workflow amplicon16S_analysis { From 913e3fafe26bdbb613a33cddba834a44084c080e Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Sat, 9 Sep 2023 10:12:08 -0400 Subject: [PATCH 13/16] skip demux_metag on dnax --- pipes/WDL/workflows/demux_metag.wdl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pipes/WDL/workflows/demux_metag.wdl b/pipes/WDL/workflows/demux_metag.wdl index 7ff1ae27a..03da06631 100644 --- a/pipes/WDL/workflows/demux_metag.wdl +++ b/pipes/WDL/workflows/demux_metag.wdl @@ -1,5 +1,7 @@ version 1.0 +#DX_SKIP_WORKFLOW + import "../tasks/tasks_demux.wdl" as demux import "../tasks/tasks_metagenomics.wdl" as metagenomics import "../tasks/tasks_read_utils.wdl" as read_utils From 5861ced19ad9ef4772f0cc739ba5477f171fde7d Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Sat, 9 Sep 2023 10:34:06 -0400 Subject: [PATCH 14/16] skip two terra-only WDLs on dnax --- pipes/WDL/workflows/terra_table_to_tsv.wdl | 2 ++ pipes/WDL/workflows/terra_update_assemblies.wdl | 2 ++ 2 files changed, 4 insertions(+) diff --git a/pipes/WDL/workflows/terra_table_to_tsv.wdl b/pipes/WDL/workflows/terra_table_to_tsv.wdl index 41987548a..a72ad6284 100644 --- a/pipes/WDL/workflows/terra_table_to_tsv.wdl +++ b/pipes/WDL/workflows/terra_table_to_tsv.wdl @@ -1,5 +1,7 @@ version 1.0 +#DX_SKIP_WORKFLOW + import "../tasks/tasks_terra.wdl" as terra workflow terra_table_to_tsv { diff --git a/pipes/WDL/workflows/terra_update_assemblies.wdl b/pipes/WDL/workflows/terra_update_assemblies.wdl index b81b266ed..4ac69137b 100644 --- a/pipes/WDL/workflows/terra_update_assemblies.wdl +++ b/pipes/WDL/workflows/terra_update_assemblies.wdl @@ -1,5 +1,7 @@ version 1.0 +#DX_SKIP_WORKFLOW + import "../tasks/tasks_terra.wdl" as terra workflow update_data_tables { From b3f05f87729210c489cf64ebda70fb5b739b8c0b Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Sat, 9 Sep 2023 10:39:10 -0400 Subject: [PATCH 15/16] yaml.load without loader deprecated, switch to safe_load --- pipes/dnax/dx-launcher/dx-yml-build | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/dnax/dx-launcher/dx-yml-build b/pipes/dnax/dx-launcher/dx-yml-build index 737329280..29d001d96 100755 --- a/pipes/dnax/dx-launcher/dx-yml-build +++ b/pipes/dnax/dx-launcher/dx-yml-build @@ -14,7 +14,7 @@ app_basename=os.path.splitext(os.path.basename(app_yaml_path))[0] output_json_filename=app_basename+'.json' with open(app_yaml_path) as infile: - data = yaml.load(infile) + data = yaml.safe_load(infile) data["00COMMENT"] = "This {}.json has been generated from {} automatically using dx-yml-build".format(app_basename,app_yaml_path) with open(output_json_filename, 'w') as outfile: json.dump(data, outfile, sort_keys=True, indent=2) From 71354ecfb28e58374e76c742bf74316115046864 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Sat, 9 Sep 2023 15:21:27 -0400 Subject: [PATCH 16/16] enable dnax deploy on github actions for dnanexus branch; fix test input --- .github/workflows/build.yml | 2 +- test/input/WDL/test_inputs-assemble_denovo-dnanexus.dx.json | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 11e271237..1b869a56f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -277,7 +277,7 @@ jobs: deploy_dnanexus: #if: ${{ github.event.ref == 'dnanexus' }} - if: github.event_name == 'release' || github.ref == 'refs/heads/master' + if: github.event_name == 'release' || github.ref == 'refs/heads/master' || github.ref == 'refs/heads/dnanexus' needs: - validate_wdl_womtool - validate_wdl_miniwdl diff --git a/test/input/WDL/test_inputs-assemble_denovo-dnanexus.dx.json b/test/input/WDL/test_inputs-assemble_denovo-dnanexus.dx.json index c182224e0..748842f99 100644 --- a/test/input/WDL/test_inputs-assemble_denovo-dnanexus.dx.json +++ b/test/input/WDL/test_inputs-assemble_denovo-dnanexus.dx.json @@ -6,7 +6,5 @@ ], "stage-common.filter_to_taxon_db": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F1zXZ9Q0pvkp7FkZ646YJX2y" } }, - "stage-common.reference_genome_fasta": [ { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F1zXZ9Q0pvkp7FkZ646YJX2y" } } ], - - "stage-common.novocraft_license": { "$dnanexus_link": { "project": "project-F89kXY805X08BpXq7xjxbX9F", "id": "file-F1zkVGQ0jy1P68J88kyJ8zVF" } } + "stage-common.reference_genome_fasta": [ { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F1zXZ9Q0pvkp7FkZ646YJX2y" } } ] }