{ | { | ||||
"{{ project_name }}.sample_id": "{{ sample_id }}", | "{{ project_name }}.sample_id": "{{ sample_id }}", | ||||
"{{ project_name }}.fastq": "{{ fastq }}", | "{{ project_name }}.fastq": "{{ fastq }}", | ||||
"{{ project_name }}.p": "{{ p }}", | |||||
"{{ project_name }}.n": "{{ n }}", | "{{ project_name }}.n": "{{ n }}", | ||||
"{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/seqkit:0.12.0", | "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/seqkit:0.12.0", | ||||
"{{ project_name }}.cluster_config": "{{ cluster_config }}", | "{{ project_name }}.cluster_config": "{{ cluster_config }}", |
String sample_id | String sample_id | ||||
File fastq | File fastq | ||||
Float? p | |||||
Int? n | |||||
Int n | |||||
String docker | String docker | ||||
String cluster_config | String cluster_config | ||||
String disk_size | String disk_size | ||||
set -o pipefail | set -o pipefail | ||||
set -e | set -e | ||||
nt=$(nproc) | nt=$(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 | |||||
# seqkit sample --two-pass --threads $nt -s 100 -p ${p} ${fastq} -o ${sample_id}.fastq.gz | |||||
seqkit sample --two-pass --threads $nt -s 100 -n ${n} ${fastq} -o ${sample_id}.fastq.gz | |||||
>>> | >>> | ||||
runtime { | runtime { |
String sample_id | String sample_id | ||||
File fastq | File fastq | ||||
Float? p | |||||
Int? n | |||||
Int n | |||||
String docker | String docker | ||||
String cluster_config | String cluster_config | ||||
String disk_size | String disk_size | ||||
input: | input: | ||||
sample_id=sample_id, | sample_id=sample_id, | ||||
fastq=fastq, | fastq=fastq, | ||||
p=p, | |||||
n=n, | n=n, | ||||
docker=docker, | docker=docker, | ||||
cluster_config=cluster_config, | cluster_config=cluster_config, |