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 { |
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 |