Awesome

bam2cram-nf

A repository to convert BAM->CRAM files

run examples

#using a tsv file, with custom working directory
nextflow run main.nf  --bam_csv test/bams.txt --fasta test/ref.fa --fai test/ref.fa.fai --output_folder csv2 -w tmp
#using a directory with bams
nextflow run main.nf --bams test --fasta test/ref.fa  --fai test/ref.fa.fai --output_folder dirs_bam

tsv file

A tabular file with the following colums:

label   bam     index
S4      /path/S4.bam       /path/S4.bam.bai
S3      /path/S3.bam       /path/S3.bam.bai

Samtools

This tool has been tested with samtools 1.11.