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bump pangolin docker #210

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merged 3 commits into from
Feb 9, 2021
Merged

bump pangolin docker #210

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4cb95a0
bump pangolin docker
dpark01 Feb 9, 2021
72935b4
fix pangolin version check
dpark01 Feb 9, 2021
6322a87
remove more optional args
dpark01 Feb 9, 2021
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8 changes: 1 addition & 7 deletions pipes/WDL/tasks/tasks_sarscov2.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -108,22 +108,17 @@ task pangolin_one_sample {
File genome_fasta
Int? min_length
Float? max_ambig
Boolean include_putative = true
}
String basename = basename(genome_fasta, ".fasta")
command {
set -e
pangolin -v > VERSION_PANGOLIN
pangolin -lv > VERSION_LINEAGES
pangolin -pv > VERSION_PANGOLEARN

pangolin "~{genome_fasta}" \
--outfile "~{basename}.pangolin_report.csv" \
-t "$(nproc)" \
--include-putative \
~{"--min-length " + min_length} \
~{"--max-ambig " + max_ambig} \
~{true="--include-putative" false="" include_putative} \
--verbose

cp "~{basename}.pangolin_report.csv" input.csv
Expand All @@ -137,15 +132,14 @@ task pangolin_one_sample {
grep ^lineage transposed.tsv | cut -f 2 | grep -v lineage > PANGOLIN_CLADE
}
runtime {
docker: "staphb/pangolin:2.1.11-pangolearn-2021-02-01"
docker: "staphb/pangolin:2.2.1-pangolearn-2021-02-06"
memory: "3 GB"
cpu: 2
disks: "local-disk 50 HDD"
dx_instance_type: "mem1_ssd1_v2_x2"
}
output {
String pangolin_version = read_string("VERSION_PANGOLIN")
String lineages_version = read_string("VERSION_LINEAGES")
String pangolearn_version = read_string("VERSION_PANGOLEARN")
File pangolin_csv = "~{basename}.pangolin_report.csv"
String pango_lineage = read_string("PANGOLIN_CLADE")
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2 changes: 1 addition & 1 deletion requirements-modules.txt
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Expand Up @@ -6,5 +6,5 @@ broadinstitute/beast-beagle-cuda=1.10.5pre
broadinstitute/ncbi-tools=2.10.7.1
nextstrain/base=build-20210127T135203Z
andersenlabapps/ivar=1.3.1
staphb/pangolin=2.1.11-pangolearn-2021-02-01
staphb/pangolin=2.2.1-pangolearn-2021-02-06
neherlab/nextclade=0.12.0