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bump to viral-core 2.1.27 #281

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Apr 30, 2021
Merged

bump to viral-core 2.1.27 #281

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4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Expand Up @@ -291,7 +291,7 @@ task align_reads {
Boolean? skip_mark_dupes = false

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"

String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
}
Expand Down Expand Up @@ -708,7 +708,7 @@ task run_discordance {
String out_basename = "run"
Int min_coverage = 4

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
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4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_demux.wdl
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Expand Up @@ -6,7 +6,7 @@ task merge_tarballs {
String out_filename

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down Expand Up @@ -142,7 +142,7 @@ task illumina_demux {
Int? maxRecordsInRam

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}
parameter_meta {
flowcell_tgz: {
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2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_interhost.wdl
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Expand Up @@ -142,7 +142,7 @@ task index_ref {
File? novocraft_license

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
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6 changes: 3 additions & 3 deletions pipes/WDL/tasks/tasks_ncbi.wdl
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Expand Up @@ -186,7 +186,7 @@ task structured_comments {

File? filter_to_ids

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}
String out_base = basename(assembly_stats_tsv, '.txt')
command <<<
Expand Down Expand Up @@ -264,7 +264,7 @@ task rename_fasta_header {

String out_basename = basename(genome_fasta, ".fasta")

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}
command {
set -e
Expand Down Expand Up @@ -447,7 +447,7 @@ task sra_meta_prep {
Boolean paired

String out_name = "sra_metadata.tsv"
String docker="quay.io/broadinstitute/viral-core:2.1.26"
String docker="quay.io/broadinstitute/viral-core:2.1.27"
}
parameter_meta {
cleaned_bam_filepaths: {
Expand Down
4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Expand Up @@ -81,7 +81,7 @@ task derived_cols {
String? lab_highlight_loc
Array[File] table_map = []

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}
parameter_meta {
lab_highlight_loc: {
Expand Down Expand Up @@ -480,7 +480,7 @@ task filter_sequences_by_length {
File sequences_fasta
Int min_non_N = 1

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}
parameter_meta {
sequences_fasta: {
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10 changes: 5 additions & 5 deletions pipes/WDL/tasks/tasks_read_utils.wdl
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Expand Up @@ -79,7 +79,7 @@ task get_sample_meta {
input {
Array[File] samplesheets_extended

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}
command <<<
python3 << CODE
Expand Down Expand Up @@ -137,7 +137,7 @@ task merge_and_reheader_bams {
File? reheader_table
String out_basename

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down Expand Up @@ -197,7 +197,7 @@ task rmdup_ubam {
String method = "mvicuna"

Int? machine_mem_gb
String? docker = "quay.io/broadinstitute/viral-core:2.1.26"
String? docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

parameter_meta {
Expand Down Expand Up @@ -251,7 +251,7 @@ task downsample_bams {
Boolean? deduplicateAfter = false

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down Expand Up @@ -310,7 +310,7 @@ task FastqToUBAM {
String? platform_name
String? sequencing_center

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}
parameter_meta {
fastq_1: { description: "Unaligned read1 file in fastq format", patterns: ["*.fastq", "*.fastq.gz", "*.fq", "*.fq.gz"] }
Expand Down
12 changes: 6 additions & 6 deletions pipes/WDL/tasks/tasks_reports.wdl
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Expand Up @@ -7,7 +7,7 @@ task alignment_metrics {
File? primers_bed

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

String out_basename = basename(aligned_bam, ".bam")
Expand Down Expand Up @@ -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:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down Expand Up @@ -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:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down Expand Up @@ -211,7 +211,7 @@ task fastqc {
input {
File reads_bam

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

String reads_basename=basename(reads_bam, ".bam")
Expand Down Expand Up @@ -244,7 +244,7 @@ task align_and_count {
Int topNHits = 3

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

String reads_basename=basename(reads_bam, ".bam")
Expand Down Expand Up @@ -289,7 +289,7 @@ task align_and_count_summary {

String output_prefix = "count_summary"

String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_taxon_filter.wdl
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Expand Up @@ -202,7 +202,7 @@ task merge_one_per_sample {
Boolean? rmdup = false

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_utils.wdl
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Expand Up @@ -204,7 +204,7 @@ task tsv_stack {
input {
Array[File]+ input_tsvs
String out_basename
String docker = "quay.io/broadinstitute/viral-core:2.1.26"
String docker = "quay.io/broadinstitute/viral-core:2.1.27"
}

command {
Expand Down
2 changes: 1 addition & 1 deletion requirements-modules.txt
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@@ -1,4 +1,4 @@
broadinstitute/viral-core=2.1.26
broadinstitute/viral-core=2.1.27
broadinstitute/viral-assemble=2.1.16.1
broadinstitute/viral-classify=2.1.16.0
broadinstitute/viral-phylo=2.1.19.1
Expand Down