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bump viral-assemble #187

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merged 2 commits into from
Dec 22, 2020
Merged

bump viral-assemble #187

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185396d
update viral-assembly
dpark01 Dec 22, 2020
22d052c
update viral-assemble to 2.1.12.1
dpark01 Dec 22, 2020
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10 changes: 5 additions & 5 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Original file line number Diff line number Diff line change
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:2.1.12.0"
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.1"
}

command {
Expand Down Expand Up @@ -80,7 +80,7 @@ task scaffold {
Float? scaffold_min_pct_contig_aligned

Int? machine_mem_gb
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.1"

# 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")
Expand Down Expand Up @@ -342,7 +342,7 @@ task refine_assembly_with_aligned_reads {
Int? min_coverage=3

Int? machine_mem_gb
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.1"
}

parameter_meta {
Expand Down Expand Up @@ -434,7 +434,7 @@ task refine {
Int? min_coverage=1

Int? machine_mem_gb
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.1"

String assembly_basename=basename(basename(assembly_fasta, ".fasta"), ".scaffold")
}
Expand Down Expand Up @@ -504,7 +504,7 @@ 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:2.1.12.0"
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.1"

# 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")
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_reports.wdl
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Expand Up @@ -436,7 +436,7 @@ task compare_two_genomes {
File genome_two
String out_basename

String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.1"
}

command {
Expand Down
2 changes: 1 addition & 1 deletion requirements-modules.txt
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@@ -1,5 +1,5 @@
broadinstitute/viral-core=2.1.12
broadinstitute/viral-assemble=2.1.12.0
broadinstitute/viral-assemble=2.1.12.1
broadinstitute/viral-classify=2.1.12.1
broadinstitute/viral-phylo=2.1.12.0
broadinstitute/beast-beagle-cuda=1.10.5pre
Expand Down