nf-core/samtools/quickcheck @ 0.0.0-0c7146d
Summary
Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and then seeks to the end of the file and checks that an end-of-file (EOF) is present and intact (BAM and CRAM only). Alignment records are not checked. The quickcheck module returns a non-zero EXIT_CODE if any input files don't have a valid header or are missing an EOF block. Otherwise EXIT_CODE is zero.
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_QUICKCHECK } from 'nf-core/samtools/quickcheck'
License
MIT License
Name
|
SAMTOOLS_QUICKCHECK |
|---|
meta
map
|
Groovy Map containing sample information. e.g. |
|---|---|
bam
file
|
sequence_trace file *.{cram,sam,bam}
|
bam
tuple
meta
map
|
Groovy Map containing sample information. e.g. |
|---|---|
bam
file
|
sequence_trace file *.{cram,sam,bam}
|
EXIT_CODE
string
|
Exit code (0 for success, non-zero otherwise) that is the result of the format check. |
versions_samtools
tuple
${task.process}
string
|
The name of the process |
|---|---|
samtools
string
|
The name of the tool |
samtools version | sed '1!d;s/.* //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | Tools for dealing with SAM, BAM and CRAM files | https://www.htslib.org/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:34:03 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fquickcheck/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/quickcheck/blobs/sha256:e5421e28e975171ad26792b828e41baebedf88d795da8a660a1d297df6dc3163 |
| Size | 3.4 KB |
| Checksum | sha256:e5421e28e975171ad26792b828e41baebedf88d795da8a660a1d297df6dc3163 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:43:21 (UTC) | 4 | 3.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:34:03 (UTC) | 4 | 3.4 KB |