Read-In Sample Sheet

[buehlere]

try running pipeline:

nextflow run main.nf --input samplsheet.csv -profile singularity --outdir ./results 

updating input to match specified sample sheet:

• edit schema of input: https://github.com/mskcc-omics-workflows/access_data_analysis/blob/main/assets/schema_input.json nextflow checks this file to see if the input is correctly formatted.

  • input parameter is declared here: https://github.com/mskcc-omics-workflows/access_data_analysis/blob/main/nextflow.config#L14

• edit the PIPELINE_INITIALISATION module to parse sample sheet correctly:

  • the module is called here: https://github.com/mskcc-omics-workflows/access_data_analysis/blob/main/main.nf#L69-L76
  • here is the part module that will need changed: https://github.com/mskcc-omics-workflows/access_data_analysis/blob/main/subworkflows/local/utils_nfcore_access_data_analysis_pipeline/main.nf#L75-L93
    • some documentation on operators: https://www.nextflow.io/docs/latest/reference/operator.html
    • the output structure we are aiming for:

[id:sample, type:tumor]
[id:sample, type:tumor]
[id:sample, type:tumor]

• check output by viewing with PIPELINE_INITIALISATION.out.samplesheet.view() here : https://github.com/mskcc-omics-workflows/access_data_analysis/blob/main/main.nf#L77.