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Bamclipper topics migration #10882

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57d4dd6
Migrate basicpy module to topic channels
santiagotariza Mar 12, 2026
bdd84ec
Migrate basicpy module to topic channel
santiagotariza Mar 12, 2026
1b16310
Merge branch 'master' into master
LouisLeNezet Mar 12, 2026
1be4c34
Update modules/nf-core/basicpy/main.nf
santiagotariza Mar 12, 2026
e2db4a0
Merge branch 'master' into master
andresferben Mar 12, 2026
f81585e
Migrate bamclipper module to topic channels
santiagotariza Mar 13, 2026
f63a995
Migrate bamclipper module to topic channels
santiagotariza Mar 13, 2026
36686ae
Fix details for bamclipper topic migration
santiagotariza Mar 13, 2026
80366ca
Apply pre-commit formatting fixes
santiagotariza Mar 13, 2026
8e18c58
Fix auto-generated empty dicts in meta.yml output schema
santiagotariza Mar 13, 2026
8378e26
Merge branch 'master' into bamclipper_topics_migration
SPPearce Mar 18, 2026
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21 changes: 4 additions & 17 deletions modules/nf-core/bamclipper/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,42 +11,29 @@ process BAMCLIPPER {
input:
tuple val(meta), path(bam), path(bai), path(bedpe)

output:
output:
tuple val(meta), path("*.primerclipped.bam") , emit: bam
tuple val(meta), path("*.primerclipped.bam.bai"), emit: bai
path "versions.yml" , emit: versions

tuple val("${task.process}"), val('bamclipper'), val("1.0.0"), emit: versions_bamclipper, topic: versions
tuple val("${task.process}"), val('samtools'), eval("samtools --version |& sed '1!d ; s/samtools //'"), emit: versions_samtools, topic: versions
// WARN: Version information not provided by tool on CLI
when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI
"""
bamclipper.sh \\
-b ${bam} \\
-p ${bedpe} \\
-n $task.cpus \\
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamclipper: $VERSION
samtools: \$( samtools --version |& sed '1!d ; s/samtools //' )
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.0.0'
"""
touch ${prefix}.primerclipped.bam
touch ${prefix}.primerclipped.bam.bai

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamclipper: $VERSION
samtools: \$( samtools --version |& sed '1!d ; s/samtools //' )
END_VERSIONS
"""
}
62 changes: 47 additions & 15 deletions modules/nf-core/bamclipper/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
name: "bamclipper"

description: This module is used to clip primer sequences from your alignments.
keywords:
- primer
Expand All @@ -8,15 +7,14 @@ keywords:
- bam
tools:
- "bamclipper":
description: "BAMClipper: removing primers from alignments to minimize false-negative
mutations in amplicon next-generation sequencing"
description: "BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing"
homepage: "https://github.com/tommyau/bamclipper"
documentation: "https://github.com/tommyau/bamclipper"
tool_dev_url: "https://github.com/tommyau/bamclipper"
doi: "10.1038/s41598-017-01703-6"
licence: ["MIT"]
license:
- "MIT"
identifier: ""

input:
- - meta:
type: map
Expand Down Expand Up @@ -45,8 +43,7 @@ output:
Groovy Map containing sample information `[ id:'sample1']`
- "*.primerclipped.bam":
type: file
description: Sorted BAM file containing clipped query sequences according
to the given primer pair locations
description: Sorted BAM file containing clipped query sequences according to the given primer pair locations
pattern: "*.primerclipped.bam"
ontologies: []
bai:
Expand All @@ -56,17 +53,52 @@ output:
Groovy Map containing sample information `[ id:'sample1']`
- "*.primerclipped.bam.bai":
type: file
description: "BAI index of the output BAM file"
description: BAI index of the output BAM file
pattern: "*.primerclipped.bam.bai"
ontologies: []
versions_bamclipper:
- - "${task.process}":
type: string
description: The name of the process
- "bamclipper":
type: string
description: The name of the tool
- "1.0.0":
type: string
description: The hardcoded version of the tool
versions_samtools:
- - "${task.process}":
type: string
description: The name of the process
- "samtools":
type: string
description: The name of the tool
- "samtools --version |& sed '1!d ; s/samtools //'":
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - "${task.process}":
type: string
description: The name of the process
- "bamclipper":
type: string
description: The name of the tool
- "1.0.0":
type: string
description: The hardcoded version of the tool
- - "${task.process}":
type: string
description: The name of the process
- "samtools":
type: string
description: The name of the tool
- "samtools --version |& sed '1!d ; s/samtools //'":
type: eval
description: The expression to obtain the version of the tool

authors:
- "@krannich479"
maintainers:
- "@krannich479"
- "@krannich479"
84 changes: 41 additions & 43 deletions modules/nf-core/bamclipper/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,51 +2,27 @@
"SarsCov2 - [BAM, BEDPE] - stub": {
"content": [
{
"0": [
"versions_bamclipper": [
[
{
"id": "MT192765.1"
},
"MT192765.1.primerclipped.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "MT192765.1"
},
"MT192765.1.primerclipped.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
"BAMCLIPPER",
"bamclipper",
"1.0.0"
]
],
"2": [
"versions.yml:md5,3f9ffa9e0acba7ec9e95087508b2fc29"
],
"bai": [
"versions_samtools": [
[
{
"id": "MT192765.1"
},
"MT192765.1.primerclipped.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
"BAMCLIPPER",
"samtools",
"samtools 1.12\nUsing htslib 1.12\nCopyright (C) 2021 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1616004847436/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1616004847436/work=/usr/local/src/conda/samtools-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure plugins=yes, plugin-path=/usr/local/libexec/htslib libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes htscodecs=1.0\n CC: /opt/conda/conda-bld/htslib_1615999655191/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1615999655191/work=/usr/local/src/conda/htslib-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t preload, data, file\n S3 Multipart Upload:\t s3w, s3w+https, s3w+http\n libcurl:\t imaps, pop3, gophers, http, smb, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, mqtt, https, smbs, tftp, pop3s, dict\n Google Cloud Storage:\t gs+http, gs+https, gs\n Amazon S3:\t s3+https, s3+http, s3\n crypt4gh-needed:\t crypt4gh\n mem:\t mem"
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@SPPearce SPPearce Mar 18, 2026

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We only want to capture 1.12 here.
This is such an old version of samtools, that maybe you'll need a different command?

]
],
"bam": [
[
{
"id": "MT192765.1"
},
"MT192765.1.primerclipped.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,3f9ffa9e0acba7ec9e95087508b2fc29"
]
}
],
"timestamp": "2026-03-13T11:47:57.492891",
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-03-20T17:07:35.685662094"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"SarsCov2 - [BAM, BEDPE]": {
"content": [
Expand All @@ -68,7 +44,18 @@
]
],
"2": [
"versions.yml:md5,3f9ffa9e0acba7ec9e95087508b2fc29"
[
"BAMCLIPPER",
"bamclipper",
"1.0.0"
]
],
"3": [
[
"BAMCLIPPER",
"samtools",
"samtools 1.12\nUsing htslib 1.12\nCopyright (C) 2021 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1616004847436/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1616004847436/work=/usr/local/src/conda/samtools-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure plugins=yes, plugin-path=/usr/local/libexec/htslib libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes htscodecs=1.0\n CC: /opt/conda/conda-bld/htslib_1615999655191/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1615999655191/work=/usr/local/src/conda/htslib-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t preload, data, file\n S3 Multipart Upload:\t s3w, s3w+https, s3w+http\n libcurl:\t imaps, pop3, gophers, http, smb, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, mqtt, https, smbs, tftp, pop3s, dict\n Google Cloud Storage:\t gs+http, gs+https, gs\n Amazon S3:\t s3+https, s3+http, s3\n crypt4gh-needed:\t crypt4gh\n mem:\t mem"
]
],
"bai": [
[
Expand All @@ -86,15 +73,26 @@
"test.paired_end.sorted.primerclipped.bam:md5,a56516da81ff46243f6154eaf6a0af35"
]
],
"versions": [
"versions.yml:md5,3f9ffa9e0acba7ec9e95087508b2fc29"
"versions_bamclipper": [
[
"BAMCLIPPER",
"bamclipper",
"1.0.0"
]
],
"versions_samtools": [
[
"BAMCLIPPER",
"samtools",
"samtools 1.12\nUsing htslib 1.12\nCopyright (C) 2021 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1616004847436/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1616004847436/work=/usr/local/src/conda/samtools-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure plugins=yes, plugin-path=/usr/local/libexec/htslib libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes htscodecs=1.0\n CC: /opt/conda/conda-bld/htslib_1615999655191/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1615999655191/work=/usr/local/src/conda/htslib-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t preload, data, file\n S3 Multipart Upload:\t s3w, s3w+https, s3w+http\n libcurl:\t imaps, pop3, gophers, http, smb, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, mqtt, https, smbs, tftp, pop3s, dict\n Google Cloud Storage:\t gs+http, gs+https, gs\n Amazon S3:\t s3+https, s3+http, s3\n crypt4gh-needed:\t crypt4gh\n mem:\t mem"
]
]
}
],
"timestamp": "2026-03-13T11:47:53.516774",
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-03-20T17:06:37.486491271"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
}
}
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