nf_coverage_demo

Nextflow demo plotting mean coverage over a series of BAM files. Two parameters are required:

• --bam_folder: folder containing BAM files
• --bed: bed file listing regions to consider to calculate coverage

Download test data set

git clone https://github.com/iarcbioinfo/data_test

Usage

Use one of the three profiles to run with docker, singularity or conda:

nextflow run iarcbioinfo/nf_coverage_demo  -profile docker --bam_folder data_test/BAM/BAM_multiple/ --bed data_test/BED/TP53_exon2_11.bed
nextflow run iarcbioinfo/nf_coverage_demo  -profile singularity --bam_folder data_test/BAM/BAM_multiple/ --bed data_test/BED/TP53_exon2_11.bed
nextflow run iarcbioinfo/nf_coverage_demo  -profile conda --bam_folder data_test/BAM/BAM_multiple/ --bed data_test/BED/TP53_exon2_11.bed