From b85522cd88eee2d54445415a48907878d2ee5789 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Thu, 29 Apr 2021 23:24:37 -0400 Subject: [PATCH 1/2] only build dnanexus on travis for master branch or PRs against master --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 83b185988..15b632574 100644 --- a/.travis.yml +++ b/.travis.yml @@ -86,6 +86,7 @@ jobs: - language: java jdk: openjdk11 stage: build + if: branch = master env: - TRAVIS_JOB=deploy_dnanexus # DX_API_TOKEN (for DNAnexus builds) -- token #3, expires 12/31/2024 From 900cd9f926c8793ac03de47237c8ffd43b12f242 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Thu, 29 Apr 2021 23:36:29 -0400 Subject: [PATCH 2/2] bump viral-core 2.1.27 to 2.1.28 --- pipes/WDL/tasks/tasks_assembly.wdl | 4 ++-- pipes/WDL/tasks/tasks_demux.wdl | 4 ++-- pipes/WDL/tasks/tasks_interhost.wdl | 2 +- pipes/WDL/tasks/tasks_ncbi.wdl | 6 +++--- pipes/WDL/tasks/tasks_nextstrain.wdl | 4 ++-- pipes/WDL/tasks/tasks_read_utils.wdl | 10 +++++----- pipes/WDL/tasks/tasks_reports.wdl | 12 ++++++------ pipes/WDL/tasks/tasks_taxon_filter.wdl | 2 +- pipes/WDL/tasks/tasks_utils.wdl | 2 +- requirements-modules.txt | 2 +- 10 files changed, 24 insertions(+), 24 deletions(-) diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl index aaf6757bd..f13cede64 100644 --- a/pipes/WDL/tasks/tasks_assembly.wdl +++ b/pipes/WDL/tasks/tasks_assembly.wdl @@ -291,7 +291,7 @@ task align_reads { Boolean? skip_mark_dupes = false Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean") } @@ -708,7 +708,7 @@ task run_discordance { String out_basename = "run" Int min_coverage = 4 - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl index ff1118b82..2a58fb385 100644 --- a/pipes/WDL/tasks/tasks_demux.wdl +++ b/pipes/WDL/tasks/tasks_demux.wdl @@ -6,7 +6,7 @@ task merge_tarballs { String out_filename Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { @@ -142,7 +142,7 @@ task illumina_demux { Int? maxRecordsInRam Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } parameter_meta { flowcell_tgz: { diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl index 67bf55f3e..3986fe74f 100644 --- a/pipes/WDL/tasks/tasks_interhost.wdl +++ b/pipes/WDL/tasks/tasks_interhost.wdl @@ -142,7 +142,7 @@ task index_ref { File? novocraft_license Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl index 973210e36..7ab529ba1 100644 --- a/pipes/WDL/tasks/tasks_ncbi.wdl +++ b/pipes/WDL/tasks/tasks_ncbi.wdl @@ -186,7 +186,7 @@ task structured_comments { File? filter_to_ids - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } String out_base = basename(assembly_stats_tsv, '.txt') command <<< @@ -264,7 +264,7 @@ task rename_fasta_header { String out_basename = basename(genome_fasta, ".fasta") - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { set -e @@ -447,7 +447,7 @@ task sra_meta_prep { Boolean paired String out_name = "sra_metadata.tsv" - String docker="quay.io/broadinstitute/viral-core:2.1.27" + String docker="quay.io/broadinstitute/viral-core:2.1.28" } parameter_meta { cleaned_bam_filepaths: { diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 9cdb38bed..0cd7ba629 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -81,7 +81,7 @@ task derived_cols { String? lab_highlight_loc Array[File] table_map = [] - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } parameter_meta { lab_highlight_loc: { @@ -480,7 +480,7 @@ task filter_sequences_by_length { File sequences_fasta Int min_non_N = 1 - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } parameter_meta { sequences_fasta: { diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl index c08573b6f..865c49607 100644 --- a/pipes/WDL/tasks/tasks_read_utils.wdl +++ b/pipes/WDL/tasks/tasks_read_utils.wdl @@ -79,7 +79,7 @@ task get_sample_meta { input { Array[File] samplesheets_extended - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command <<< python3 << CODE @@ -137,7 +137,7 @@ task merge_and_reheader_bams { File? reheader_table String out_basename - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { @@ -197,7 +197,7 @@ task rmdup_ubam { String method = "mvicuna" Int? machine_mem_gb - String? docker = "quay.io/broadinstitute/viral-core:2.1.27" + String? docker = "quay.io/broadinstitute/viral-core:2.1.28" } parameter_meta { @@ -251,7 +251,7 @@ task downsample_bams { Boolean? deduplicateAfter = false Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { @@ -310,7 +310,7 @@ task FastqToUBAM { String? platform_name String? sequencing_center - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } parameter_meta { fastq_1: { description: "Unaligned read1 file in fastq format", patterns: ["*.fastq", "*.fastq.gz", "*.fq", "*.fq.gz"] } diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index c9875d649..03d4953bb 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -7,7 +7,7 @@ task alignment_metrics { File? primers_bed Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } String out_basename = basename(aligned_bam, ".bam") @@ -77,7 +77,7 @@ task plot_coverage { Boolean bin_large_plots = false String? binning_summary_statistic = "max" # max or min - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { @@ -152,7 +152,7 @@ task coverage_report { Array[File] mapped_bam_idx # optional.. speeds it up if you provide it, otherwise we auto-index String out_report_name = "coverage_report.txt" - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { @@ -211,7 +211,7 @@ task fastqc { input { File reads_bam - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } String reads_basename=basename(reads_bam, ".bam") @@ -244,7 +244,7 @@ task align_and_count { Int topNHits = 3 Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } String reads_basename=basename(reads_bam, ".bam") @@ -289,7 +289,7 @@ task align_and_count_summary { String output_prefix = "count_summary" - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { diff --git a/pipes/WDL/tasks/tasks_taxon_filter.wdl b/pipes/WDL/tasks/tasks_taxon_filter.wdl index b7feeae57..6e919ec54 100644 --- a/pipes/WDL/tasks/tasks_taxon_filter.wdl +++ b/pipes/WDL/tasks/tasks_taxon_filter.wdl @@ -202,7 +202,7 @@ task merge_one_per_sample { Boolean? rmdup = false Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { diff --git a/pipes/WDL/tasks/tasks_utils.wdl b/pipes/WDL/tasks/tasks_utils.wdl index a1aaa4a3a..2009abe54 100644 --- a/pipes/WDL/tasks/tasks_utils.wdl +++ b/pipes/WDL/tasks/tasks_utils.wdl @@ -204,7 +204,7 @@ task tsv_stack { input { Array[File]+ input_tsvs String out_basename - String docker = "quay.io/broadinstitute/viral-core:2.1.27" + String docker = "quay.io/broadinstitute/viral-core:2.1.28" } command { diff --git a/requirements-modules.txt b/requirements-modules.txt index 16d49475e..19be2b62c 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -1,4 +1,4 @@ -broadinstitute/viral-core=2.1.27 +broadinstitute/viral-core=2.1.28 broadinstitute/viral-assemble=2.1.16.1 broadinstitute/viral-classify=2.1.16.0 broadinstitute/viral-phylo=2.1.19.1