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Added version print statements to all tasks. #6

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merged 7 commits into from
Oct 27, 2023
Merged

Added version print statements to all tasks. #6

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edee46d
Added version print statements to all tasks.
williamrowell May 20, 2023
74d14fa
CommandShellCheck, SC2046 Quote this to prevent word splitting.
williamrowell May 20, 2023
bc86fa6
update wdl-ci config file after successful tests
github-actions[bot] May 20, 2023
c631102
Fix htsbox version command.
williamrowell May 20, 2023
28d0011
update wdl-ci config file after successful tests
github-actions[bot] May 20, 2023
8cf587a
Merge branch 'develop' into feature/print_versions
gconcepcion Oct 26, 2023
894094f
update wdl-ci config file after successful tests
github-actions[bot] Oct 26, 2023
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12 changes: 6 additions & 6 deletions wdl-ci.config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@
"tasks": {
"parse_families": {
"key": "parse_families",
"digest": "fczc72mlu6iw3glecpbme5jj4ceqyqtw",
"digest": "rprxafsnidgno35awynatngwbnuw6suo",
"tests": [
{
"inputs": {
Expand All @@ -137,7 +137,7 @@
},
"yak_count": {
"key": "yak_count",
"digest": "6hlh6n3b3cqohtmjweg57of626he4c4v",
"digest": "i4jt54vu25mhikalp47febetx7mn6xmo",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -175,7 +175,7 @@
"tasks": {
"hifiasm_assemble": {
"key": "hifiasm_assemble",
"digest": "vhkzwee3f754jcjksog22uyps3j6myow",
"digest": "yt7mrvhlur5xzn5sxbhe52kvvu6r4ejr",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -232,7 +232,7 @@
},
"gfa2fa": {
"key": "gfa2fa",
"digest": "es7l5kyje3fiy5vxjnnsqg4fw6sitmdo",
"digest": "drs64xxuazexpb6n6glhbkmartzdorbj",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -264,7 +264,7 @@
},
"align_hifiasm": {
"key": "align_hifiasm",
"digest": "4qf5jeepfn3jv3g2socql6xh7vmd4b7s",
"digest": "ctgtjbeekxz2xcq42jnuyxhsfnrb52xg",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -299,7 +299,7 @@
"tasks": {
"htsbox": {
"key": "htsbox",
"digest": "hgv6puzttllbwzgmunnigqiopcq3gl7x",
"digest": "wzaxerbnwe327lejeyudsposw4ywor7t",
"tests": [
{
"inputs": {
Expand Down
12 changes: 12 additions & 0 deletions workflows/assemble_genome/assemble_genome.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,8 @@ task hifiasm_assemble {
command <<<
set -euo pipefail

echo "hifiasm version: $(hifiasm --version)"

hifiasm \
-o ~{prefix} \
-t ~{threads} \
Expand Down Expand Up @@ -152,16 +154,22 @@ task gfa2fa {
command <<<
set -euo pipefail

echo "gfatools version: $(gfatools version)"

gfatools gfa2fa \
~{gfa} \
> ~{gfa_basename}.fasta

bgzip --version

bgzip \
--threads ~{threads} \
--stdout \
~{gfa_basename}.fasta \
> ~{gfa_basename}.fasta.gz

echo "calN50.js version: $(k8 /opt/calN50/calN50.js -v)"

# Calculate assembly stats
k8 \
/opt/calN50/calN50.js \
Expand Down Expand Up @@ -208,6 +216,10 @@ task align_hifiasm {
command <<<
set -euo pipefail

echo "minimap2 version: $(minimap2 --version)"

samtools --version

minimap2 \
-t ~{threads - 4} \
-L \
Expand Down
3 changes: 3 additions & 0 deletions workflows/de_novo_assembly_sample/de_novo_assembly_sample.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,9 @@ task htsbox {
# Ensure the sample is named based on the bam basename (not the full path)
cp ~{bam} .

# htsbox has no version option; grep the version from the help output; ignore errors
htsbox 2>&1 | grep -Eo 'Version: htslib [0-9a-z-]+, htsbox [0-9a-z-]+' || true

htsbox pileup \
-q20 \
-c \
Expand Down
6 changes: 5 additions & 1 deletion workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,8 @@ task parse_families {
command <<<
set -euo pipefail

parse_cohort.py --version

parse_cohort.py \
--cohort_json ~{cohort_json} \
--parse_families
Expand All @@ -147,7 +149,7 @@ task parse_families {
}

runtime {
docker: "~{runtime_attributes.container_registry}/parse-cohort@sha256:94444e7e3fd151936c9bbcb8a64b6a5e7d8c59de53b256a83f15c4ea203977b4"
docker: "~{runtime_attributes.container_registry}/parse-cohort@sha256:e6a8ac24ada706644e62878178790a0006db9a6abec7a312232052bb0666fe8f"
cpu: 2
memory: "4 GB"
disk: "20 GB"
Expand Down Expand Up @@ -177,6 +179,8 @@ task yak_count {
command <<<
set -euo pipefail

echo "yak version: $(yak version)"

yak count \
-t ~{threads} \
-o ~{sample_id}.yak \
Expand Down