diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl index dc0e53ecc..678478069 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:2.1.20.0" + String docker="quay.io/broadinstitute/viral-assemble:2.1.16.1" } command { @@ -80,7 +80,7 @@ task scaffold { Float? scaffold_min_pct_contig_aligned Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-assemble:2.1.20.0" + String docker="quay.io/broadinstitute/viral-assemble:2.1.16.1" # 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") @@ -295,7 +295,7 @@ task align_reads { Boolean? skip_mark_dupes=false Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean") } @@ -411,7 +411,7 @@ task refine_assembly_with_aligned_reads { Int? min_coverage=3 Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-assemble:2.1.20.0" + String docker="quay.io/broadinstitute/viral-assemble:2.1.16.1" } parameter_meta { @@ -510,7 +510,7 @@ task refine { Int? min_coverage=1 Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-assemble:2.1.20.0" + String docker="quay.io/broadinstitute/viral-assemble:2.1.16.1" String assembly_basename=basename(basename(assembly_fasta, ".fasta"), ".scaffold") } @@ -580,7 +580,7 @@ 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:2.1.20.0" + String docker="quay.io/broadinstitute/viral-assemble:2.1.16.1" # 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") @@ -712,7 +712,7 @@ task run_discordance { String out_basename = "run" Int min_coverage=4 - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl index 5bd353e11..4dbf3ffa8 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:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -98,10 +98,9 @@ task illumina_demux { String? runStartDate Int? maxReadsInRamPerTile Int? maxRecordsInRam - Boolean? forceGC=true Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } parameter_meta { flowcell_tgz: { @@ -240,7 +239,6 @@ task illumina_demux { $max_records_in_ram \ --JVMmemory="$mem_in_mb"m \ $demux_threads \ - ~{true='--force_gc=true' false="--force_gc=false" forceGC} \ --append_run_id \ --compression_level=5 \ --out_meta_by_sample meta_by_sample.json \ diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl index 9ab7d31aa..77c05a2b9 100644 --- a/pipes/WDL/tasks/tasks_interhost.wdl +++ b/pipes/WDL/tasks/tasks_interhost.wdl @@ -9,7 +9,7 @@ task multi_align_mafft_ref { Float? mafft_gapOpeningPenalty Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } String fasta_basename = basename(reference_fasta, '.fasta') @@ -53,7 +53,7 @@ task multi_align_mafft { Float? mafft_gapOpeningPenalty Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } command { @@ -142,7 +142,7 @@ task index_ref { File? novocraft_license Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -252,7 +252,7 @@ task merge_vcfs_gatk { File ref_fasta Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" String output_prefix = "merged" } diff --git a/pipes/WDL/tasks/tasks_intrahost.wdl b/pipes/WDL/tasks/tasks_intrahost.wdl index 3e60e418e..6ca16ed31 100644 --- a/pipes/WDL/tasks/tasks_intrahost.wdl +++ b/pipes/WDL/tasks/tasks_intrahost.wdl @@ -11,7 +11,7 @@ task isnvs_per_sample { Boolean removeDoublyMappedReads=true Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" String sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped") } @@ -52,7 +52,7 @@ task isnvs_vcf { Boolean naiveFilter=false Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } parameter_meta { @@ -125,7 +125,7 @@ task annotate_vcf_snpeff { String? emailAddress Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" String output_basename = basename(basename(in_vcf, ".gz"), ".vcf") } diff --git a/pipes/WDL/tasks/tasks_metagenomics.wdl b/pipes/WDL/tasks/tasks_metagenomics.wdl index 3b81bf198..c59ff7e11 100644 --- a/pipes/WDL/tasks/tasks_metagenomics.wdl +++ b/pipes/WDL/tasks/tasks_metagenomics.wdl @@ -11,7 +11,7 @@ task krakenuniq { File krona_taxonomy_db_tgz # taxonomy.tab Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } parameter_meta { @@ -136,7 +136,7 @@ task build_krakenuniq_db { Int? zstd_compression_level Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } command { @@ -202,7 +202,7 @@ task kraken2 { Int? min_base_qual Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } parameter_meta { @@ -334,7 +334,7 @@ task build_kraken2_db { Int? zstd_compression_level Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } parameter_meta { @@ -472,7 +472,7 @@ task blastx { File krona_taxonomy_db_tgz Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } parameter_meta { @@ -559,7 +559,7 @@ task krona { Int? magnitude_column Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } command { @@ -658,7 +658,7 @@ task filter_bam_to_taxa { String out_filename_suffix = "filtered" Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } String out_basename = basename(classified_bam, ".bam") + "." + out_filename_suffix @@ -743,7 +743,7 @@ task kaiju { File krona_taxonomy_db_tgz # taxonomy/taxonomy.tab Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } String input_basename = basename(reads_unmapped_bam, ".bam") diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl index c7efe382d..ff45f0567 100644 --- a/pipes/WDL/tasks/tasks_ncbi.wdl +++ b/pipes/WDL/tasks/tasks_ncbi.wdl @@ -25,7 +25,7 @@ task download_fasta { Array[String]+ accessions String emailAddress - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } command { @@ -56,7 +56,7 @@ task download_annotations { String emailAddress String combined_out_prefix - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } command { @@ -100,7 +100,7 @@ task annot_transfer { File reference_fasta Array[File]+ reference_feature_table - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } parameter_meta { @@ -153,7 +153,7 @@ task align_and_annot_transfer_single { Array[File]+ reference_fastas Array[File]+ reference_feature_tables - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } parameter_meta { @@ -205,7 +205,7 @@ task structured_comments { File? filter_to_ids - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } String out_base = basename(assembly_stats_tsv, '.txt') command <<< @@ -283,7 +283,7 @@ task rename_fasta_header { String out_basename = basename(genome_fasta, ".fasta") - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { set -e @@ -421,7 +421,7 @@ task sra_meta_prep { Boolean paired String out_name = "sra_metadata.tsv" - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } parameter_meta { cleaned_bam_filepaths: { @@ -583,7 +583,7 @@ task biosample_to_genbank { File? filter_to_ids Boolean s_dropout_note=true - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } String base = basename(biosample_attributes, ".txt") command { @@ -635,7 +635,7 @@ task prepare_genbank { String? assembly_method_version Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker="quay.io/broadinstitute/viral-phylo:2.1.19.1" } parameter_meta { diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 032d3ced8..9ac945755 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -126,7 +126,7 @@ task derived_cols { String? lab_highlight_loc Array[File] table_map=[] - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } parameter_meta { lab_highlight_loc: { @@ -541,7 +541,7 @@ task filter_sequences_by_length { File sequences_fasta Int min_non_N = 1 - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } parameter_meta { sequences_fasta: { @@ -690,7 +690,7 @@ task mafft_one_chr { Boolean large = false Boolean memsavetree = false - String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.0" + String docker = "quay.io/broadinstitute/viral-phylo:2.1.19.1" Int mem_size = 500 Int cpus = 64 } diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl index d3de8a743..228b69374 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:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } 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:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -197,7 +197,7 @@ task rmdup_ubam { String method="mvicuna" Int? machine_mem_gb - String? docker="quay.io/broadinstitute/viral-core:2.1.20" + String? docker="quay.io/broadinstitute/viral-core:2.1.19" } parameter_meta { @@ -251,7 +251,7 @@ task downsample_bams { Boolean? deduplicateAfter=false Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -310,7 +310,7 @@ task FastqToUBAM { String? platform_name String? sequencing_center - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } 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 ab82628a7..82f6b2463 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -6,7 +6,7 @@ task alignment_metrics { File ref_fasta File? primers_bed - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } String out_basename = basename(aligned_bam, ".bam") @@ -73,7 +73,7 @@ task plot_coverage { Boolean bin_large_plots=false String? binning_summary_statistic="max" # max or min - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -148,7 +148,7 @@ 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:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -207,7 +207,7 @@ task fastqc { input { File reads_bam - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } String reads_basename=basename(reads_bam, ".bam") @@ -240,7 +240,7 @@ task align_and_count { Int topNHits = 3 Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } String reads_basename=basename(reads_bam, ".bam") @@ -285,7 +285,7 @@ task align_and_count_summary { String output_prefix="count_summary" - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -316,7 +316,7 @@ task aggregate_metagenomics_reports { String aggregate_taxlevel_focus = "species" Int aggregate_top_N_hits = 5 - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } parameter_meta { @@ -524,7 +524,7 @@ task tsv_stack { input { Array[File]+ input_tsvs String out_basename - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { @@ -554,7 +554,7 @@ task compare_two_genomes { File genome_two String out_basename - String docker="quay.io/broadinstitute/viral-assemble:2.1.20.0" + String docker="quay.io/broadinstitute/viral-assemble:2.1.16.1" } command { diff --git a/pipes/WDL/tasks/tasks_taxon_filter.wdl b/pipes/WDL/tasks/tasks_taxon_filter.wdl index b5c15eff4..3de90f735 100644 --- a/pipes/WDL/tasks/tasks_taxon_filter.wdl +++ b/pipes/WDL/tasks/tasks_taxon_filter.wdl @@ -14,7 +14,7 @@ task deplete_taxa { Int? cpu=8 Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } parameter_meta { @@ -110,7 +110,7 @@ task filter_to_taxon { String? neg_control_prefixes_space_separated = "neg water NTC" Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } # do this in two steps in case the input doesn't actually have "cleaned" in the name @@ -166,7 +166,7 @@ task build_lastal_db { File sequences_fasta Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-classify:2.1.20.0" + String docker="quay.io/broadinstitute/viral-classify:2.1.16.0" } String db_name = basename(sequences_fasta, ".fasta") @@ -202,7 +202,7 @@ task merge_one_per_sample { Boolean? rmdup=false Int? machine_mem_gb - String docker="quay.io/broadinstitute/viral-core:2.1.20" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } command { diff --git a/requirements-modules.txt b/requirements-modules.txt index 828a87893..a4a002d9f 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -1,7 +1,7 @@ -broadinstitute/viral-core=2.1.20 -broadinstitute/viral-assemble=2.1.20.0 -broadinstitute/viral-classify=2.1.20.0 -broadinstitute/viral-phylo=2.1.20.0 +broadinstitute/viral-core=2.1.19 +broadinstitute/viral-assemble=2.1.16.1 +broadinstitute/viral-classify=2.1.16.0 +broadinstitute/viral-phylo=2.1.19.1 broadinstitute/beast-beagle-cuda=1.10.5pre broadinstitute/ncbi-tools=2.10.7.1 nextstrain/base=build-20210318T204019Z