nf-core/bam2fastx/bam2fastq @ 0.0.0-0c7146d
Summary
Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data
Get started
Add the following snippet to your workflow script to include this module.
include { BAM2FASTX_BAM2FASTQ } from 'nf-core/bam2fastx/bam2fastq'
License
MIT License
Process
Name
|
BAM2FASTX_BAM2FASTQ |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
PacBio BAM file *.bam
|
index
file
|
PacBio BAM file index (.pbi) *.pbi
|
Output
2 channels
#1
fastq
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.fastq.gz
file
|
Gzipped FASTQ file *.fastq.gz
|
#2
versions_bam2fastx
tuple
${task.process}
string
|
The name of the process |
|---|---|
bam2fastx
string
|
The name of the tool |
bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bam2fastx | Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files | https://github.com/PacificBiosciences/bam2fastx |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 18:44:06 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbam2fastx%2Fbam2fastq/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bam2fastx/bam2fastq/blobs/sha256:237aade3c5a6a108f89d2171b715959efa86a0d844934675bd58f192587fcde7 |
| Size | 2.2 KB |
| Checksum | sha256:237aade3c5a6a108f89d2171b715959efa86a0d844934675bd58f192587fcde7 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:03:16 (UTC) | 3 | 2.2 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:02:34 (UTC) | 4 | 2.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:44:06 (UTC) | 3 | 2.2 KB |