Bayesian reconstruction of ancient DNA fragments
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
Unaligned BAM or one or two gzipped FASTQ file(s)
*.{bam,fq.gz,fastq.gz}
bam{:bash}
${prefix}.bam{:bash}
BAM file
*.bam
fq_pass{:bash}
${prefix}.fq.gz{:bash}
Trimmed and merged FASTQ
*.fq.gz
fq_fail{:bash}
${prefix}.fail.fq.gz{:bash}
Failed trimmed and merged FASTQs
*.fail.fq.gz
unmerged_r1_fq_pass{:bash}
${prefix}_r1.fq.gz{:bash}
Passed unmerged R1 FASTQs
*.r1.fq.gz
unmerged_r1_fq_fail{:bash}
${prefix}_r1.fail.fq.gz{:bash}
Failed unmerged R1 FASTQs
*.r1.fail.fq.gz
unmerged_r2_fq_pass{:bash}
${prefix}_r2.fq.gz{:bash}
Passed unmerged R2 FASTQs
*.r2.fq.gz
unmerged_r2_fq_fail{:bash}
${prefix}_r2.fail.fq.gz{:bash}
Failed unmerged R2 FASTQs
*.r2.fail.fq.gz
log{:bash}
*.log{:bash}
Log file of command
*.log
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
