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feat: add n and threads

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YaqingLiu 1 jaar geleden
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2 gewijzigde bestanden met toevoegingen van 12 en 4 verwijderingen
  1. +9
    -3
      tasks/DownSample.wdl
  2. +3
    -1
      workflow.wdl

+ 9
- 3
tasks/DownSample.wdl Bestand weergeven



String sample_id String sample_id
File fastq File fastq
Float p
Float? p
Int? n
String docker String docker
String cluster_config String cluster_config
String disk_size String disk_size
command <<< command <<<
set -o pipefail set -o pipefail
set -e set -e
seqkit sample --two-pass -s 100 -p ${p} ${fastq} -o ${sample_id}.fastq.gz
nt=$(nproc)
if [ ${p} ]; then
seqkit sample --two-pass --threads ${nt} -s 100 -p ${p} ${fastq} -o ${sample_id}.fastq.gz
else
seqkit sample --two-pass --threads ${nt} -s 100 -n ${n} ${fastq} -o ${sample_id}.fastq.gz
fi
>>> >>>


runtime { runtime {

+ 3
- 1
workflow.wdl Bestand weergeven

String sample_id String sample_id
File fastq File fastq
Float p
Float? p
Int? n
String docker String docker
String cluster_config String cluster_config
String disk_size String disk_size
sample_id=sample_id, sample_id=sample_id,
fastq=fastq, fastq=fastq,
p=p, p=p,
n=n,
docker=docker, docker=docker,
cluster_config=cluster_config, cluster_config=cluster_config,
disk_size=disk_size disk_size=disk_size

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