3 changed files with 5 additions and 5 deletions
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inputs
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| { | { | ||||
| "{{ project_name }}.sample_id": {{ sample_id | tojson }}, | |||||
| "{{ project_name }}.sample_id": "{{ sample_id }}", | |||||
| "{{ project_name }}.fastq1": {{ fastq1 | tojson }}, | "{{ project_name }}.fastq1": {{ fastq1 | tojson }}, | ||||
| "{{ project_name }}.fastq2": {{ fastq2 | tojson }}, | "{{ project_name }}.fastq2": {{ fastq2 | tojson }}, | ||||
| "{{ project_name }}.subsampling_rate": "{{ subsampling_rate }}", | "{{ project_name }}.subsampling_rate": "{{ subsampling_rate }}", |
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tasks/ngscheckmate_fastq.wdl
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| task ngscheckmate_fastq { | task ngscheckmate_fastq { | ||||
| String output_id | |||||
| File fq1 | File fq1 | ||||
| File fq2 | File fq2 | ||||
| String basename(fq1, "_R1.fastq.gz") | |||||
| String subsampling_rate | String subsampling_rate | ||||
| String docker | String docker | ||||
| String cluster_config | String cluster_config |
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workflow.wdl
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| workflow {{ project_name }} { | workflow {{ project_name }} { | ||||
| Array[String] sample_id | |||||
| String sample_id | |||||
| Array[File] fastq1 | Array[File] fastq1 | ||||
| Array[File] fastq2 | Array[File] fastq2 | ||||
| String subsampling_rate | String subsampling_rate | ||||
| String cluster_config | String cluster_config | ||||
| String disk_size | String disk_size | ||||
| scatter (idx in range(length(sample_id))) { | |||||
| scatter (idx in range(length(fastq1))) { | |||||
| call ngscheckmate_fastq.ngscheckmate_fastq as ngscheckmate_fastq { | call ngscheckmate_fastq.ngscheckmate_fastq as ngscheckmate_fastq { | ||||
| input: | input: | ||||
| output_id=sample_id[idx], | |||||
| fq1=fastq1[idx], | fq1=fastq1[idx], | ||||
| fq2=fastq2[idx], | fq2=fastq2[idx], | ||||
| subsampling_rate=subsampling_rate, | subsampling_rate=subsampling_rate, |
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