Non-destructive & Informative scan of a NextFlow work folder
./scanMyWorkDir.sh <pipelineDir-nf>
$ ./scanMyWorkDir.sh gatk4-fromUBAMtoCallableBAM-nf/
Scanning gatk4-fromUBAMtoCallableBAM-nf/ Nexflow work directory for suffix outputs........................................................................done!
Top ten suffixes that are eating up disk space in gatk4-fromUBAMtoCallableBAM-nf :
1 18G *.fastq
2 18G *.aln.bam
3 16G *.recal.bam
4 12G *.aln.dup.bam
5 22M *.aln.bam.bai
6 15M *.recal.bai
7 15M *.aln.dup.bam.bai
8 2.6M *.recal_stats/qualimapReport.html
9 2.2M *.recal_data.table
10 688K *.recal_stats/qualimapReportOutsideRegions.html
Try these commands to further investigate (and maybe rm, who knows) :
├── find gatk4-fromUBAMtoCallableBAM-nf/work/ -name *.fastq -type f
└── ls -lrh --sort=size gatk4-fromUBAMtoCallableBAM-nf/work/*/*/*.fastq