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expose optional input parameter disk_size for kraken2 standalone wfs #316

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merged 7 commits into from
Feb 8, 2024
Merged

expose optional input parameter disk_size for kraken2 standalone wfs #316

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ea7f048
expose optional input parameter disk_size for kraken2 standalone task…
kapsakcj Jan 23, 2024
d9dffbc
update CI
kapsakcj Jan 23, 2024
0105912
update 2 GH actions workflows to use actions/checkout@v4 from v3 to s…
kapsakcj Jan 24, 2024
a76d78b
upgrade to actions/upload-artifact@v4 to squash warning about node.js…
kapsakcj Jan 24, 2024
7874d06
Merge remote-tracking branch 'origin/main' into cjk-kraken-standalone…
kapsakcj Feb 7, 2024
8d265d9
add kraken_disk_size and kraken_memory as optional inputs to both PE …
kapsakcj Feb 7, 2024
625388b
update CI
kapsakcj Feb 7, 2024
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3 changes: 2 additions & 1 deletion tasks/taxon_id/task_kraken2.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ task kraken2_standalone {
String unclassified_out = "unclassified#.fastq"
Int mem = 32
Int cpu = 4
Int disk_size = 100
}
command <<<
echo $(kraken2 --version 2>&1) | sed 's/^.*Kraken version //;s/ .*$//' | tee VERSION
Expand Down Expand Up @@ -138,7 +139,7 @@ task kraken2_standalone {
docker: "~{docker}"
memory: "~{mem} GB"
cpu: cpu
disks: "local-disk 100 SSD"
disks: "local-disk " + disk_size + " SSD"
preemptible: 0
}
}
2 changes: 1 addition & 1 deletion tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
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Expand Up @@ -627,7 +627,7 @@
- path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
md5sum: 4e1d4f6b8085a209f9721748a0c0fef0
- path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl
md5sum: 164c9186746bfc4c89907a43af56328c
md5sum: 37a1bccc53b5ff8e1968f07a85bb328f
- path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
md5sum: faacd87946ee3fbdf70f3a15b79ce547
- path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
Expand Down
4 changes: 2 additions & 2 deletions tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
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Expand Up @@ -592,7 +592,7 @@
- path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
md5sum: 4e1d4f6b8085a209f9721748a0c0fef0
- path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl
md5sum: 164c9186746bfc4c89907a43af56328c
md5sum: 37a1bccc53b5ff8e1968f07a85bb328f
- path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl
md5sum: faacd87946ee3fbdf70f3a15b79ce547
- path: miniwdl_run/wdl/tasks/utilities/task_broad_terra_tools.wdl
Expand All @@ -602,6 +602,6 @@
- path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
md5sum: 90eb6ac7463058a81da77120aa45138b
- path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
md5sum: 891579890a8a46d794d0cc9dee38c29a
md5sum: 10e8a4bad676c1a5eedf01f65bc70fda
- path: miniwdl_run/workflow.log
contains: ["wdl", "theiaprok_illumina_se", "NOTICE", "done"]
6 changes: 5 additions & 1 deletion workflows/utilities/wf_read_QC_trim_pe.wdl
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Expand Up @@ -25,6 +25,8 @@ workflow read_QC_trim_pe {
Boolean call_midas = false
File? midas_db
Boolean call_kraken = false
Int? kraken_disk_size
Int? kraken_memory
File? kraken_db
String? target_org
File? adapters
Expand Down Expand Up @@ -132,7 +134,9 @@ workflow read_QC_trim_pe {
samplename = samplename,
read1 = read1_raw,
read2 = read2_raw,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken_db]),
disk_size = kraken_disk_size,
mem = kraken_memory
}
}
}
Expand Down
6 changes: 5 additions & 1 deletion workflows/utilities/wf_read_QC_trim_se.wdl
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Expand Up @@ -28,6 +28,8 @@ workflow read_QC_trim_se {
File? midas_db
Boolean call_kraken = false
File? kraken_db
Int? kraken_disk_size
Int? kraken_memory
String read_processing = "trimmomatic" # options: trimmomatic, fastp
String read_qc = "fastq_scan" # options: fastq_scan, fastqc
String fastp_args = "-g -5 20 -3 20"
Expand Down Expand Up @@ -104,7 +106,9 @@ workflow read_QC_trim_se {
input:
samplename = samplename,
read1 = read1_raw,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken_db]),
disk_size = kraken_disk_size,
mem = kraken_memory
}
}
}
Expand Down