--input |
Read file glob used when no samplesheet is provided |
data/reads/*.fasta.gz |
--samplesheet |
CSV with sample,reads,chromosome,gff,tss,cpg,repeatmasker |
null |
--reference |
Reference FASTA/FASTA.GZ |
data/ref/hg38_partial.fasta.gz |
--query_size |
Max query records passed to match.pl; 0 means all |
10 |
--chromosome |
Default chromosome label in non-samplesheet mode |
chr1 |
--annotation_dir |
Annotation directory |
data/annotations |
--gff |
GFF3 path override |
${annotation_dir}/hg38_chr1_geneannotation.gff3.gz |
--tss |
TSS table path override |
${annotation_dir}/hg38_chr1_tss.txt.gz |
--cpg |
CpG table path override |
${annotation_dir}/hg38_cpg.txt.gz |
--repeatmasker |
RepeatMasker path override |
${annotation_dir}/hg38_repeatmasker.bed.gz |
--outdir |
Published output directory |
results |
--publish_mode |
Nextflow publish mode |
copy |
--tracedir |
Optional explicit run-metadata directory |
${outdir}/pipeline_info |