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dpark01dpark01
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Merge pull request #650 from broadinstitute/bump-viral-ngs
bump viral-ngs 3.0.10, remove GATK IndelRealigner deps, update lofreq pipeline
2 parents eec1073 + 6c3555f commit f251675

16 files changed

+143
-127
lines changed

‎.github/workflows/build.yml‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -48,9 +48,9 @@ jobs:
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runs-on: ubuntu-24.04
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steps:
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- name: checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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# fetch git tags (tagged releases) because
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# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
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# actions/checkout@v6 does either a full checkout or a shallow checkout without tags
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- name: fetch tags
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run: git fetch --prune --unshallow --tags
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- name: Programmatic environment setup
@@ -80,7 +80,7 @@ jobs:
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run: |
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env
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- name: install python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: '3.10'
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- name: install system dependencies
@@ -103,9 +103,9 @@ jobs:
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runs-on: ubuntu-24.04
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steps:
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- name: checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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# fetch git tags (tagged releases) because
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# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
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# actions/checkout@v6 does either a full checkout or a shallow checkout without tags
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- name: fetch tags
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run: git fetch --prune --unshallow --tags
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- name: Programmatic environment setup
@@ -131,7 +131,7 @@ jobs:
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echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
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echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
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- name: install java
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uses: actions/setup-java@v4
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uses: actions/setup-java@v5
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with:
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distribution: 'temurin'
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java-version: '17'
@@ -155,9 +155,9 @@ jobs:
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runs-on: ubuntu-24.04
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steps:
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- name: checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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# fetch git tags (tagged releases) because
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# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
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# actions/checkout@v6 does either a full checkout or a shallow checkout without tags
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- name: fetch tags
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run: git fetch --prune --unshallow --tags
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- name: Programmatic environment setup
@@ -183,7 +183,7 @@ jobs:
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echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
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echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
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- name: install python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: '3.10'
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- name: install docs dependencies
@@ -202,9 +202,9 @@ jobs:
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runs-on: ubuntu-24.04
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steps:
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- name: checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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# fetch git tags (tagged releases) because
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# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
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# actions/checkout@v6 does either a full checkout or a shallow checkout without tags
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- name: fetch tags
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run: git fetch --prune --unshallow --tags
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- name: Programmatic environment setup
@@ -237,7 +237,7 @@ jobs:
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sudo rm -rf "/usr/local/share/boost"
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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- name: install java
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uses: actions/setup-java@v4
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uses: actions/setup-java@v5
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with:
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distribution: 'temurin'
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java-version: '17'
@@ -259,9 +259,9 @@ jobs:
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runs-on: ubuntu-24.04
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steps:
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- name: checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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# fetch git tags (tagged releases) because
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# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
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# actions/checkout@v6 does either a full checkout or a shallow checkout without tags
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- name: fetch tags
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run: git fetch --prune --unshallow --tags
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- name: Programmatic environment setup
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sudo rm -rf "/usr/local/share/boost"
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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- name: install python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: '3.10'
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- name: install system dependencies
@@ -305,7 +305,7 @@ jobs:
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run: |
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pip3 install miniwdl docker[tls] six
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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uses: docker/setup-buildx-action@v4
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- name: test with miniwdl
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shell: bash
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run: |
@@ -330,9 +330,9 @@ jobs:
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DX_PROJECT: project-F8PQ6380xf5bK0Qk0YPjB17P
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steps:
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- name: checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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# fetch git tags (tagged releases) because
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# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
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# actions/checkout@v6 does either a full checkout or a shallow checkout without tags
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- name: fetch tags
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run: git fetch --prune --unshallow --tags
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- name: Programmatic environment setup
@@ -363,11 +363,11 @@ jobs:
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echo "${{ github.event.action }}"
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echo "${{ github.event.pull_request.merged }}"
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- name: install python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: '3.10'
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- name: install java
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uses: actions/setup-java@v4
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uses: actions/setup-java@v5
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with:
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distribution: 'temurin'
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java-version: '17'

‎pipes/WDL/tasks/tasks_assembly.wdl‎

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Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ task assemble {
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Int? machine_mem_gb
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Int? cpu
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-assemble"
19+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
2020
}
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parameter_meta{
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reads_unmapped_bam: {
@@ -124,7 +124,7 @@ task select_references {
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Int? skani_c
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Int? skani_n
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127-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-assemble"
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
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Int machine_mem_gb = 4
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Int cpu = 2
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Int disk_size = 100
@@ -223,7 +223,7 @@ task scaffold {
223223
Float? scaffold_min_pct_contig_aligned
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Int? machine_mem_gb
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String docker="quay.io/broadinstitute/viral-ngs:3.0.9-assemble"
226+
String docker="quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
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# do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
229229
String sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
@@ -475,7 +475,7 @@ task skani_triangle {
475475
Int compression_factor = 10
476476
Int min_aligned_frac = 15
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478-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-assemble"
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
479479
Int machine_mem_gb = 8
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Int cpu = 4
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Int disk_size = 100
@@ -636,7 +636,7 @@ task ivar_trim_stats {
636636
String out_basename = "ivar_trim_stats"
637637
String flowcell = ""
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639-
String docker = "quay.io/broadinstitute/py3-bio:0.1.4"
639+
String docker = "quay.io/broadinstitute/py3-bio:0.1.5"
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}
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parameter_meta {
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ivar_trim_stats_tsv: {
@@ -715,7 +715,7 @@ task align_reads {
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Int? cpu
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Int? machine_mem_gb
718-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
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String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
721721
}
@@ -724,10 +724,6 @@ task align_reads {
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# 7x input BAM to account for bbnorm preprocessing temp file
725725
Int disk_size = ceil((7 * size(reads_unmapped_bam, "GB") + 2 * size(reference_fasta, "GB") + 100) / 750.0) * 750
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727-
# Skip indel realignment for large BAMs (>1GB) to save runtime
728-
Float reads_bam_size_gb = size(reads_unmapped_bam, "GB")
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Boolean skip_realign = reads_bam_size_gb >= 1.0
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# bbnorm preprocessing: max output reads is half the downsample threshold
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Int bbnorm_max_output_reads = read_count_downsample_threshold / 2
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@@ -808,7 +804,6 @@ task align_reads {
808804
--aligner ~{aligner} \
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~{'--aligner_options "' + aligner_options + '"'} \
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~{true='--skipMarkDupes' false="" skip_mark_dupes} \
811-
~{true='--skipRealign' false="" skip_realign} \
812807
--JVMmemory "$mem_in_mb"m \
813808
~{"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
814809
--loglevel=DEBUG
@@ -883,7 +878,7 @@ task refine_assembly_with_aligned_reads {
883878
Int min_coverage = 3
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885880
Int machine_mem_gb = 8
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-assemble"
881+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
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}
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Int disk_size = 375
@@ -1019,7 +1014,7 @@ task run_discordance {
10191014
String out_basename = "run"
10201015
Int min_coverage = 4
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1022-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
10231018
}
10241019
parameter_meta {
10251020
reads_aligned_bam: {
@@ -1266,7 +1261,7 @@ task wgsim {
12661261
Int? random_seed
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Int machine_mem_gb = 7
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-assemble"
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
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}
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parameter_meta {

‎pipes/WDL/tasks/tasks_demux.wdl‎

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Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ task merge_tarballs {
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String out_filename
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
9+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
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}
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Int disk_size = 2625
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9797
input {
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File old_sheet
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Boolean revcomp=true
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String docker = "quay.io/broadinstitute/py3-bio:0.1.4"
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String docker = "quay.io/broadinstitute/py3-bio:0.1.5"
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}
102102
String new_base = basename(basename(old_sheet, '.txt'), '.tsv')
103103
Int disk_size = 50
@@ -179,7 +179,7 @@ task illumina_demux {
179179
Int? machine_mem_gb
180180
# Note: GCP local SSDs must be allocated in pairs (2, 4, 8, 16, 24 × 375GB), so use 3000 (8 SSDs) instead of 2625 (7 SSDs)
181181
Int disk_size = 3000
182-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
182+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
183183
}
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parameter_meta {
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817817
String? sequencing_center
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
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String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
821821
}
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823823
parameter_meta {
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920920
Int? machine_mem_gb
921921
Int max_cpu = 32 # Maximum CPU cap for autoscaling (use 16 for 2-barcode, 64 for 3-barcode)
922922
Int disk_size = 750
923-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
923+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
924924
}
925925

926926
# Calculate total input size for autoscaling
@@ -1048,7 +1048,7 @@ task merge_demux_metrics {
10481048
input {
10491049
Array[File]+ metrics_files
10501050
String output_filename = "merged_demux_metrics.txt"
1051-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
1051+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
10521052
}
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10541054
parameter_meta {

‎pipes/WDL/tasks/tasks_interhost.wdl‎

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Original file line numberDiff line numberDiff line change
@@ -160,7 +160,7 @@ task multi_align_mafft_ref {
160160
Float? mafft_gapOpeningPenalty
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162162
Int? machine_mem_gb
163-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-phylo"
163+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
164164
}
165165

166166
String fasta_basename = basename(reference_fasta, '.fasta')
@@ -206,7 +206,7 @@ task multi_align_mafft {
206206
Float? mafft_gapOpeningPenalty
207207

208208
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209-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-phylo"
209+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
210210
}
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212212
Int disk_size = 200
@@ -348,7 +348,7 @@ task index_ref {
348348
File? novocraft_license
349349

350350
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351-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-core"
351+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
352352
}
353353

354354
Int disk_size = 100
@@ -470,7 +470,7 @@ task merge_vcfs_gatk {
470470
File ref_fasta
471471

472472
Int? machine_mem_gb
473-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.9-phylo"
473+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
474474

475475
String output_prefix = "merged"
476476
}

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