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allow docker image pinning to be skipped with #skip-global-version-pin annotation #493

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merged 1 commit into from
Oct 17, 2023
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allow docker image pinning to be skipped with #skip-global-version-pin annotation #493

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2 changes: 1 addition & 1 deletion github_actions_ci/check-wdl-runtimes.sh
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Expand Up @@ -12,7 +12,7 @@ for task_file in $(ls -1 pipes/WDL/tasks/*.wdl); do
OLD_TAG=$module
NEW_TAG="$module:$version"

offending_lines="$(grep -nE "^[^#]*$OLD_TAG" "${task_file}" | grep -v $NEW_TAG)"
offending_lines="$(grep -nE "^[^#]*$OLD_TAG" "${task_file}" | grep -v '#skip-global-version-pin' | grep -v $NEW_TAG)"

# if the expected tag is not seen, let us know the file and exit
if [ $? -eq 0 ]; then
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16 changes: 12 additions & 4 deletions github_actions_ci/version-wdl-runtimes.sh
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@@ -1,13 +1,21 @@
#!/bin/bash

# use sed to replace version strings of docker images based on versions defined in txt file

#
# skip this replacement for any version string line with the comment "#skip-global-version-pin"
#
# requires $MODULE_VERSIONS to be set to point to a text file with equal-sign-separated values
# export MODULE_VERSIONS="./requirements-modules.txt" && ./github_actions_ci/check-wdl-runtimes.sh

printf "Updating docker image tags in WDL files with those in ${MODULE_VERSIONS}\n\n"

while IFS='=' read module version; do
OLD_TAG=$module
NEW_TAG="$module:$version"
echo Replacing $OLD_TAG with $NEW_TAG in all task WDL files
sed -i '' "s|$OLD_TAG[^\"\']*|$NEW_TAG|g" pipes/WDL/tasks/*.wdl
done < $MODULE_VERSIONS
NEW_TAG_BOLD="$module:$(tput bold)$version$(tput sgr0)"
printf "Replacing: %-14s \n with tag: %-14s \n\n" "$OLD_TAG" "$NEW_TAG_BOLD"

sed -i '' "/^\(.*\)[[:space:]]*#skip-global-version-pin[[:space:]]*$/!s|$OLD_TAG[^\"\']*|$NEW_TAG|g" pipes/WDL/tasks/*.wdl
done < $MODULE_VERSIONS

printf "Replacements skipped for lines marked with '#skip-global-version-pin' \n\n"
4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_metagenomics.wdl
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Expand Up @@ -11,7 +11,7 @@ task krakenuniq {
File krona_taxonomy_db_tgz # taxonomy.tab

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0" #skip-global-version-pin
}

Int disk_size = 750
Expand Down Expand Up @@ -143,7 +143,7 @@ task build_krakenuniq_db {
Int? zstd_compression_level

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0" #skip-global-version-pin
}

Int disk_size = 750
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3 changes: 2 additions & 1 deletion pipes/WDL/tasks/tasks_nextstrain.wdl
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Expand Up @@ -847,7 +847,8 @@ task filter_sequences_to_list {
Array[File]? keep_list

String out_fname = sub(sub(basename(sequences, ".zst"), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
String docker = "quay.io/broadinstitute/viral-core:2.1.33" # "nextstrain/base:build-20211012T204409Z"
# Prior docker image: "nextstrain/base:build-20211012T204409Z"
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
Int disk_size = 750
}
parameter_meta {
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