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Merge branch 'master' into ct-demux-deplete-merge-lanes
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tomkinsc authored Jan 5, 2024
2 parents 45cec20 + e95b378 commit e4c0321
Showing 17 changed files with 718 additions and 78 deletions.
22 changes: 22 additions & 0 deletions .dockstore.yml
Original file line number Diff line number Diff line change
@@ -144,6 +144,11 @@ workflows:
primaryDescriptorPath: /pipes/WDL/workflows/downsample.wdl
testParameterFiles:
- empty.json
- name: dump_gcloud_env_info
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/dump_gcloud_env_info.wdl
testParameterFiles:
- empty.json
- name: fastq_to_ubam
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/fastq_to_ubam.wdl
@@ -254,6 +259,11 @@ workflows:
primaryDescriptorPath: /pipes/WDL/workflows/nextclade_single.wdl
testParameterFiles:
- empty.json
- name: reconstruct_from_alignments
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/reconstruct_from_alignments.wdl
testParameterFiles:
- empty.json
- name: sarscov2_batch_relineage
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_batch_relineage.wdl
@@ -369,3 +379,15 @@ workflows:
primaryDescriptorPath: /pipes/WDL/workflows/bam_to_qiime.wdl
testParameterFiles:
- empty.json

- name: create_enterics_qc_viz
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz.wdl
testParameterFiles:
- empty.json

- name: create_enterics_qc_viz_general
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz_general.wdl
testParameterFiles:
- empty.json
1 change: 1 addition & 0 deletions .github/workflows/build.yml
Original file line number Diff line number Diff line change
@@ -2,6 +2,7 @@ name: "viral-pipelines CI"

on:
push:
merge_group:
pull_request:
branches:
- master
2 changes: 1 addition & 1 deletion github_actions_ci/version-wdl-runtimes.sh
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
# 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
# export MODULE_VERSIONS="./requirements-modules.txt" && ./github_actions_ci/version-wdl-runtimes.sh

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

2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_assembly.wdl
Original file line number Diff line number Diff line change
@@ -517,7 +517,7 @@ task align_reads {
reports.py fastqc ~{sample_name}.mapped.bam ~{sample_name}.mapped_fastqc.html --out_zip ~{sample_name}.mapped_fastqc.zip
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
output {
5 changes: 3 additions & 2 deletions pipes/WDL/tasks/tasks_demux.wdl
Original file line number Diff line number Diff line change
@@ -159,6 +159,7 @@ task illumina_demux {
Int? threads
String? runStartDate
Int? maxRecordsInRam
Int? numberOfNegativeControls
Int? machine_mem_gb
Int disk_size = 2625
@@ -337,7 +338,7 @@ task illumina_demux {
--out_runinfo runinfo.json \
--loglevel=DEBUG
illumina.py guess_barcodes --expected_assigned_fraction=0 barcodes.txt metrics.txt barcodes_outliers.txt
illumina.py guess_barcodes ~{'--number_of_negative_controls ' + numberOfNegativeControls} --expected_assigned_fraction=0 barcodes.txt metrics.txt barcodes_outliers.txt
illumina.py flowcell_metadata --inDir $FLOWCELL_DIR flowcellMetadataFile.tsv
@@ -388,7 +389,7 @@ task illumina_demux {
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg | cut -f 3 -d ' ' > LOAD_15M
set +o pipefail
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
output {
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