From a108e82d6f90b24e57c1b89c76abadcd9a980e72 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 11 Mar 2024 14:20:51 -0400 Subject: [PATCH 1/2] bump viral-assemble from 2.2.4.0 to 2.3.0.0 --- pipes/WDL/tasks/tasks_assembly.wdl | 8 ++++---- pipes/WDL/tasks/tasks_reports.wdl | 2 +- requirements-modules.txt | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl index 8a1a11a69..ae5c2693d 100644 --- a/pipes/WDL/tasks/tasks_assembly.wdl +++ b/pipes/WDL/tasks/tasks_assembly.wdl @@ -15,7 +15,7 @@ task assemble { String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt") Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-assemble:2.2.4.0" + String docker = "quay.io/broadinstitute/viral-assemble:2.3.0.0" } parameter_meta{ reads_unmapped_bam: { @@ -122,7 +122,7 @@ task scaffold { Float? scaffold_min_pct_contig_aligned Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-assemble:2.2.4.0" + String docker="quay.io/broadinstitute/viral-assemble:2.3.0.0" # do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name String sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades") @@ -586,7 +586,7 @@ task refine_assembly_with_aligned_reads { Int min_coverage = 3 Int machine_mem_gb = 15 - String docker = "quay.io/broadinstitute/viral-assemble:2.2.4.0" + String docker = "quay.io/broadinstitute/viral-assemble:2.3.0.0" } Int disk_size = 375 @@ -711,7 +711,7 @@ task refine_2x_and_plot { String? plot_coverage_novoalign_options = "-r Random -l 40 -g 40 -x 20 -t 100 -k" Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-assemble:2.2.4.0" + String docker = "quay.io/broadinstitute/viral-assemble:2.3.0.0" # do this in two steps in case the input doesn't actually have "cleaned" in the name String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned") diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index 3c9b192fa..e2a046be7 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -674,7 +674,7 @@ task compare_two_genomes { File genome_two String out_basename - String docker = "quay.io/broadinstitute/viral-assemble:2.2.4.0" + String docker = "quay.io/broadinstitute/viral-assemble:2.3.0.0" } Int disk_size = 50 diff --git a/requirements-modules.txt b/requirements-modules.txt index 53718d00a..27f7396bf 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -1,5 +1,5 @@ broadinstitute/viral-core=2.3.0 -broadinstitute/viral-assemble=2.2.4.0 +broadinstitute/viral-assemble=2.3.0.0 broadinstitute/viral-classify=2.2.4.0 broadinstitute/viral-phylo=2.1.20.2 broadinstitute/py3-bio=0.1.2 From 1a25392c515bdc59f1378b7d64e9caa0f82f3478 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 11 Mar 2024 15:39:12 -0400 Subject: [PATCH 2/2] quiet down some deprecation warnings from ghactions --- .github/workflows/build.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 20e870208..ee9281fcc 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -116,7 +116,7 @@ jobs: echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV - name: install java - uses: actions/setup-java@v3 + uses: actions/setup-java@v4 with: distribution: 'adopt' java-version: '11' @@ -218,7 +218,7 @@ jobs: sudo rm -rf "/usr/local/share/boost" sudo rm -rf "$AGENT_TOOLSDIRECTORY" - name: install java - uses: actions/setup-java@v3 + uses: actions/setup-java@v4 with: distribution: 'adopt' java-version: '11' @@ -275,7 +275,7 @@ jobs: - name: install python uses: actions/setup-python@v5 with: - python-version: '3.8' + python-version: '3.10' - name: install system dependencies run: | sudo apt-get update @@ -284,7 +284,7 @@ jobs: run: | pip3 install miniwdl docker[tls] six - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 + uses: docker/setup-buildx-action@v3 - name: test with miniwdl shell: bash run: | @@ -341,7 +341,7 @@ jobs: with: python-version: '3.8' - name: install java - uses: actions/setup-java@v3 + uses: actions/setup-java@v4 with: distribution: 'adopt' java-version: '11'