4 fichiers modifiés avec 5 ajouts et 6 suppressions
inputSamplesFileExamples.csv → input_samples.tsv
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+ 1
- 1
inputs
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| @@ -1,5 +1,5 @@ | |||
| { | |||
| "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}", | |||
| "{{ project_name }}.samples_file": "{{ samples_file }}", | |||
| "{{ bed_file }}".bed_file: "oss://pgx-reference-data/reference/bedtools/ERVmap_v2_all_sorted.bed", | |||
| "{{ project_name }}.bedtools.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", | |||
| "{{ project_name }}.bedtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1", | |||
+ 1
- 2
tasks/bedtools.wdl
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| @@ -24,7 +24,6 @@ task multiqc { | |||
| } | |||
| output { | |||
| File multiqc_html = "multiqc_report.html" | |||
| Array[File] multiqc_txt = glob("multiqc_data/*") | |||
| File read_count = "revread_count.txt" | |||
| } | |||
| } | |||
+ 3
- 3
workflow.wdl
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| @@ -2,11 +2,11 @@ import "./tasks/bedtools.wdl" as bedtools | |||
| workflow {{ project_name }} { | |||
| File inputSamplesFile | |||
| File samples_file | |||
| File bed_file | |||
| Array[Array[File]] inputSamples = read_tsv(inputSamplesFile) | |||
| Array[Array[File]] samples_file = read_tsv(samples_file) | |||
| scatter (sample in inputSamples) { | |||
| scatter (sample in samples_file) { | |||
| call bedtools.bedtools as bedtools { | |||
| input: | |||
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