kallisto/kallisto_index
kallisto
index
Description
Build a Kallisto index for the transcriptome to use Kallisto in the mapping-based mode.
Input
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Path to a FASTA-file containing the transcriptome sequences, either in plain text or compressed (.gz) format. |
--d_list | file | Path to a FASTA-file containing sequences to mask from quantification. |
Output
Name | Type & Properties | Description |
|---|---|---|
--index | file output |
Options
Name | Type & Properties | Description |
|---|---|---|
--kmer_size | integer | Kmer length passed to indexing step of pseudoaligners (default: '31'). |
--make_unique | boolean_true | Replace repeated target names with unique names. |
--aa | boolean_true | Generate index from a FASTA-file containing amino acid sequences. |
--distiguish | boolean_true | Generate index where sequences are distinguished by the sequence names. |
--min_size -m | integer | Length of minimizers (default: automatically chosen). |
--ec_max_size -e | integer | Maximum number of targets in an equivalence class (default: no maximum). |
--tmp -T | string | Path to a directory for temporary files. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
index: "$id.$key.index.Kallisto_index"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.2 \
-main-script target/nextflow/kallisto/kallisto_index/main.nf \
-params-file params.yaml Relationships
Used by
3 relationships, 2 components
Current component
kallisto/kallisto_indexbiobox v0.4.2
Uses
0 relationships
No component dependencies found.