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README.md

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General settings

To configure this workflow, modify config/config.yaml according to your needs, following the explanations provided in the file.

Sample sheet

Add samples to config/samples.tsv. For each sample, the columns sample, type and platform have to be defined. The columns matched_normal and purity are only needed for tumor samples.

  • The sample column contains the name of a specific biological sample.
  • The type (normal, tumor) will be used to differentiate between multiple conditions of the same biological entity (e.g. a sinlge patient).
  • matched_normal should contain the sample name of the corresponding normal sample to a tumor sample.
  • purity should contain an estimated purity value for the tumor sample in the range of ]0.0, 1.0].

Unit sheet

For each sample, add one or more sequencing units (runs, lanes or replicates) to the unit sheet config/units.tsv. By activating or deactivating mergeReads in the config/config.yaml, you can decide wether to merge replicates or run them individually.

  • Each unit has a column unit which can be e.g. a running number, or an actual run, lane or replicate id.
  • Each unit has a column sample which refers to the biological sample of the unit.
  • For each unit, define either one (column fq1) or two (columns fq1, fq2) FASTQ files (these can point to anywhere in your system). Alternatively, you can define an SRA (sequence read archive) accession (starting with e.g. ERR or SRR) by using a column sra. In the latter case, the pipeline will automatically download the corresponding paired end reads from SRA. If both local files and SRA accession are available, the local files will be preferred.
  • Define adapters in the adapters column, by putting cutadapt arguments in quotation marks (e.g. "-a ACGCGATCG -A GCTAGCGTACT").

Missing values can be specified by empty columns or by writing NA. Lines can be commented out with #.

netMHC configuration

For the use of netMHCpan and netMHCIIpan, you need to install the software manually by downloading them separately following instructions at https://services.healthtech.dtu.dk/software.php. Once you have downloaded and extracted the provided folders, follow the instructions to customise the netMHCpan or netMHCIIpan file. To call the correct installation of netMHC, please give the path to the netMHC folder in corresponding field of the config.yaml, e.g. path/to/netMHCpan-4.1.