Parameters
| Parameter |
Type |
Default |
Description |
--input |
string |
(required) |
Path to the samplesheet CSV |
--outdir |
string |
results |
Directory for output files |
ICEscreen
| Parameter |
Type |
Default |
Description |
--phylum |
string |
bacillota |
Taxonomic phylum; controls the detection mode file used |
--codon_table |
integer |
11 |
NCBI genetic code for CDS translation |
--icescreen_root |
string |
auto-detect |
Path to the ICEscreen installation; overrides ICESCREEN_ROOT |
--icescreen_db |
string |
null |
Override path to pre-indexed databases (BLAST + HMM) |
icescreen_root is resolved in order: --icescreen_root parameter → ICESCREEN_ROOT environment variable →
~/repo/icescreen → /opt/icescreen.
BLASTP
| Parameter |
Type |
Default |
Description |
--blastp_evalue |
float |
0.001 |
E-value threshold for BLASTP hits |
--blastp_max_target_seqs |
integer |
10 |
Maximum number of target sequences per query |
Mobile element detection
| Parameter |
Type |
Default |
Description |
--min_cds_between_segments |
integer |
100 |
Minimum CDS count allowed between two ME segments |
--max_cds_for_ime_size |
integer |
10 |
Maximum CDS count for classifying an element as an IME |
Generic options
| Parameter |
Type |
Default |
Description |
--publish_dir_mode |
string |
copy |
Nextflow publishDir mode: copy, symlink, move, etc. |
--monochrome_logs |
boolean |
false |
Disable ANSI colour in log output |
--help |
boolean |
false |
Display the help message and exit |
--version |
boolean |
false |
Display the pipeline version and exit |