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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:10:25 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fquickcheck/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/quickcheck/blobs/sha256:bd3557c8692c8ff648a9946a4748ac6f61e457e36029dafa3644119cd0ade1e1 |
| Size | 3.4 KB |
| Checksum | sha256:bd3557c8692c8ff648a9946a4748ac6f61e457e36029dafa3644119cd0ade1e1 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:25 (UTC) | 1 | 3.4 KB | - |