bedtools/bedtools_bamtofastq
Conversion
BAM
FASTQ
Description
Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input BAM file to be converted to FASTQ. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--fastq -fq | file required output | Output FASTQ file. |
--fastq2 -fq2 | file output | FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name is creating paired FASTQ. |
Options
Name | Type & Properties | Description |
|---|---|---|
--tags | boolean_true | Create FASTQ based on the mate info in the BAM R2 and Q2 tags. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
fastq: "$id.$key.fastq"
fastq2: "$id.$key.fastq2"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.2.0 \
-main-script target/nextflow/bedtools/bedtools_bamtofastq/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_bamtofastqbiobox v0.2.0
Uses
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No component dependencies found.