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build and container updates #526

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merged 2 commits into from
Mar 12, 2024
Merged

build and container updates #526

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a108e82
bump viral-assemble from 2.2.4.0 to 2.3.0.0
dpark01 Mar 11, 2024
1a25392
quiet down some deprecation warnings from ghactions
dpark01 Mar 11, 2024
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10 changes: 5 additions & 5 deletions .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ jobs:
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: install java
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
distribution: 'adopt'
java-version: '11'
Expand Down Expand Up @@ -218,7 +218,7 @@ jobs:
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: install java
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
distribution: 'adopt'
java-version: '11'
Expand Down Expand Up @@ -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
Expand All @@ -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: |
Expand Down Expand Up @@ -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'
Expand Down
8 changes: 4 additions & 4 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Expand Up @@ -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: {
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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")
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_reports.wdl
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Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion requirements-modules.txt
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@@ -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
Expand Down