csv2fasta
Description
Convert two columns from a CSV file to FASTA entries. The CSV file can
contain an optional header and each row (other than the header) becomes
a single FASTA record. One of the two columns will be used as the names
for the FASTA entries, while the other become the sequences. The sequences
column must only contain characters that are valid IUPAC notation for
nucleotides or a group thereof (wildcard characters).
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | CSV file to be processed. |
--header | boolean_true | Parse the first line of the CSV file as a header. |
CSV dialect options
Name | Type & Properties | Description |
|---|---|---|
--delimiter | string | Overwrite the column delimiter character. |
--quote_character | string | Overwrite the character used to denote the start and end of a quoted item. |
CSV column arguments
Name | Type & Properties | Description |
|---|---|---|
--sequence_column | string | Name of the column containing the sequences. Implies 'header'. Cannot be used together with 'sequence_column_index'. |
--name_column | string | Name of the column describing the FASTA headers. Implies 'header'. Cannot be used together with 'name_column_index'. |
--sequence_column_index | integer | Index of the column to use as the FASTA sequences, counter from the left and starting from 0. Cannot be used in combination with the 'sequence_column' argument. |
--name_column_index | integer | Index of the column to use as the FASTA headers, counter from the left and starting from 0. Cannot be used in combination with 'name_column'. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file output | Output fasta file. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.fasta"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/craftbox.git \
-revision v0.3.3 \
-main-script target/nextflow/csv2fasta/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
csv2fastacraftbox v0.3.3
Uses
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