This pipeline is designed to streamline samplesheet creation for the various pipelines used in the neoantigen prediction workflow
The only inputs required are a samplesheet with some basic information (see example below), the path to input base directory (used for building file paths), and the path to the output directory where the generated samplesheets will be stored
patient_id,sample_id,specimen_id,wes_version,rnaseq_version,germline_version,sex,hla
262622,germline,085-R,2.0.2.51.0,2.0.2.21.0,2.0.1.10.0,female,A*24:02;A*30:04;B*44:03;B*57:01;C*06:02;C*07:06
262622,ORIGINATOR,085-R,2.0.2.51.0,2.0.2.21.0,2.0.1.10.0,female,A*24:02;A*30:04;B*44:03;B*57:01;C*06:02;C*07:06
262622,E3E,085-R,2.0.2.51.0,2.0.2.21.0,2.0.1.10.0,female,A*24:02;A*30:04;B*44:03;B*57:01;C*06:02;C*07:06
262622,E3EN35P99V29,085-R,2.0.2.51.0,2.0.2.21.0,2.0.1.10.0,female,A*24:02;A*30:04;B*44:03;B*57:01;C*06:02;C*07:06
262622,E3EN35P99V29T15,085-R,2.0.2.51.0,2.0.2.21.0,2.0.1.10.0,female,A*24:02;A*30:04;B*44:03;B*57:01;C*06:02;C*07:06