abhi18av / samplesheetgen-clj

A Babashka (Clojure) utility for generating samplesheets for different platforms from a base samplesheet

samplesheetgen-clj

A Babashka (Clojure) utility for generating samplesheets (CSV) for different platforms from a base samplesheet, designed with Nextflow and nf-core samplesheet practices in mind

The use case is with generation of path-specific samplesheets starting from a base samplesheet

• Input samplesheet

sample_id,fastq_1,fastq_2
study-001,001_R1.fastq.gz,001_R2.fastq.gz
study-002,002_R1.fastq.gz,002_R2.fastq.gz
study-003,003_R1.fastq.gz,

• Use samplesheetgen.bb.clj script (assuming you have babashka installed)

$ samplesheetgen.bb.clj csv \
  -i samplesheet_base.csv \
  -o samplesheet.googlestrage.csv \
  -p "gs:my-bucket"

• The new samplesheet would look like

sample_id,fastq_1,fastq_2
study-001,gs:my-bucket/001_R1.fastq.gz,gs:my-bucket/001_R2.fastq.gz
study-002,gs:my-bucket/002_R1.fastq.gz,gs:my-bucket/002_R2.fastq.gz
study-003,gs:my-bucket/003_R1.fastq.gz,