Description

Sort SAM/BAM/CRAM file

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

fasta (file)

Reference genome fasta file

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

crai (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

stats (file)

File containing samtools stats output

*.{stats}

flagstat (file)

File containing samtools flagstat output

*.{flagstat}

idxstats (file)

File containing samtools idxstats output

*.{idxstats}

versions (file)

File containing software versions

versions.yml
included in
atacseq circrna cutandrun magmap metatdenovo nascent phageannotator riboseq rnaseq rnasplice scnanoseq smrnaseq viralrecon
included modules and subworkflows
samtools/sort samtools/index samtools/stats samtools/idxstats samtools/flagstat bam_stats_samtools
maintainers
Github user drpatelh
Github user ewels
get in touch
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