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- metadata:
- sample_annotation: sandro_annotation.csv
- output_dir: /scratch/nv4e/sandro_looper_results/{sample_name}
- pipelines_dir: [../pipeline/pipeline_interface.yaml]
- sample_name,library,sample_name_1_read,sample_name_2_read,output_folder
- abeta_24h_1,RNA-seq,read1,read2,out
- abeta_24h_2,RNA-seq,read1,read2,out
- abeta_24h_3,RNA-seq,read1,read2,out
- ...
- pipelines:
- sandro_rna_seq:
- name: sandro_rna_seq
- path: sandro_rna_seq.py # relative to this
- pipeline_interface.yaml file
- looper_args: True
- arguments:
- "-S": sample_name
- "--input": sample_name_1_read
- "-O": output_folder
- ...
- ...
- derived_columns: [sample_name_1_read,sample_name_2_read,output_folder]
- data_sources:
- read1: /scratch/nv4e/sandro_looper/data/merged/{sample_name}_r1.fq.gz
- read2: /scratch/nv4e/sandro_looper/data/merged/{sample_name}_r2.fq.gz
- out: /scratch/nv4e/sandro_looper_results/results_pipeline/{sample_name}
- ...
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