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config.json
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config.json
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{
"analysis_type":"", # Name of the excel sheet in metadata
"analysis": "", # Name of the folder that will contain the output files
"metadata":"", # Path to metadata including name of the metadata
"descriptive_sentence": "", # Description of the run to print the top of the multiQC report
"read_type":["_R1_001","_R2_001"], # can be _R1 and _R2
"sequencer": "", # Nextseq2000, Nextseq500, Novaseq, SP_NextSeq, Miseq
"annotation":"", # Path to the gtf file including name of the file
"star_index":"/sps/bioaster.new/Data/Genomes/H.sapiens/GRCh38.77/Gencode_V37/STAR_index_2.7.9a", # Path to the STAR index
"transcripts":"", # Path to the fasta transcript file
"bed":"", # Path to the bed annotation file including name of the file
"tmp_dir": "", # Path to a temporary directory
"tmp_sortmerna": "", # Path to a temporary directory
"db_rRNA": "", # Path to all fasta rfam and silva files, separated by a comma
"globin_index":"", # Path to the index created from transcripts annotated as globin
"multiqc_param": "" # can be empty. Use this to pass an parameter to multiqc with -c "Path to multiqc_config.yaml"
}