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iarcbioinfo/nf_coverage_demo

Sponsored OSS

By International Agency for Research on Cancer

•Updated about 6 years ago

nf_coverage_demo automated build

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iarcbioinfo/nf_coverage_demo repository overview

⁠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

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932.3 MB

Last updated

about 8 years ago

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