Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update CENTRIFUGE: bump versions, fix missing args, and command formatting #7205

Open
wants to merge 10 commits into
base: master
Choose a base branch
from
Open

Update CENTRIFUGE: bump versions, fix missing args, and command formatting #7205

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
691393e
bump versions and fix missing args and command formatting
jfy133 Dec 12, 2024
82de233
Merge branch 'master' into update-centrifuge-version
jfy133 Dec 12, 2024
8ffe826
Merge branch 'master' into update-centrifuge-version
sateeshperi Dec 13, 2024
3644e04
CI: docker self hosted - userEmulate and dont fixOwnership
sateeshperi Dec 13, 2024
560b888
try suggestion from claude
sateeshperi Dec 13, 2024
493e821
fix cgroup parent slice
sateeshperi Dec 13, 2024
23bb3f6
rm cgroup parent slice
sateeshperi Dec 13, 2024
9049769
rm security opts
sateeshperi Dec 13, 2024
5833643
userns n security opts
sateeshperi Dec 13, 2024
28de288
Merge branch 'master' into update-centrifuge-version
jfy133 Dec 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion modules/nf-core/centrifuge/build/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::centrifuge=1.0.4.1
- bioconda::centrifuge=1.0.4.2
28 changes: 15 additions & 13 deletions modules/nf-core/centrifuge/build/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
process CENTRIFUGE_BUILD {
tag "$meta.id"
tag "${meta.id}"
label 'process_high'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
: 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"

input:
tuple val(meta), path(fasta)
Expand All @@ -15,8 +15,8 @@ process CENTRIFUGE_BUILD {
path size_table

output:
tuple val(meta), path("${prefix}/") , emit: cf
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}/"), emit: cf
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -29,13 +29,15 @@ process CENTRIFUGE_BUILD {
mkdir ${prefix}

centrifuge-build \\
-p $task.cpus \\
$fasta \\
-p ${task.cpus} \\
${fasta} \\
${prefix}/${prefix} \\
--conversion-table $conversion_table \\
--taxonomy-tree $taxonomy_tree \\
--name-table $name_table \\
${size_table_cmd}
--conversion-table ${conversion_table} \\
--taxonomy-tree ${taxonomy_tree} \\
--name-table ${name_table} \\
${size_table_cmd} \\
${args} \\


cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -44,7 +46,7 @@ process CENTRIFUGE_BUILD {
"""

stub:
def args = task.ext.args ?: ''
def _args = task.ext.args ?: ''
jfy133 marked this conversation as resolved.
Show resolved Hide resolved
prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir -p ${prefix}/
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/centrifuge/build/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,9 +80,9 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-02-15T10:10:19.439629103"
"timestamp": "2024-12-12T10:38:44.613715625"
}
}
3 changes: 2 additions & 1 deletion modules/nf-core/centrifuge/centrifuge/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::centrifuge=1.0.4.1
- bioconda::centrifuge=1.0.4.2
42 changes: 22 additions & 20 deletions modules/nf-core/centrifuge/centrifuge/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
process CENTRIFUGE_CENTRIFUGE {
tag "$meta.id"
tag "${meta.id}"
label 'process_high'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
: 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"

input:
tuple val(meta), path(reads)
Expand All @@ -14,26 +14,27 @@ process CENTRIFUGE_CENTRIFUGE {
val save_aligned

output:
tuple val(meta), path('*report.txt') , emit: report
tuple val(meta), path('*results.txt') , emit: results
tuple val(meta), path('*.{sam,tab}') , optional: true, emit: sam
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
path "versions.yml" , emit: versions
tuple val(meta), path('*report.txt'), emit: report
tuple val(meta), path('*results.txt'), emit: results
tuple val(meta), path('*.{sam,tab}'), optional: true, emit: sam
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_mapped
tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_unmapped
path "versions.yml", emit: versions
jfy133 marked this conversation as resolved.
Show resolved Hide resolved

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def unaligned = ''
def aligned = ''
if (meta.single_end) {
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
} else {
}
else {
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
}
Expand All @@ -49,13 +50,13 @@ process CENTRIFUGE_CENTRIFUGE {
centrifuge \\
-x \$db_name \\
--temp-directory ./temp \\
-p $task.cpus \\
$paired \\
-p ${task.cpus} \\
${paired} \\
--report-file ${prefix}.report.txt \\
-S ${prefix}.results.txt \\
$unaligned \\
$aligned \\
$args
${unaligned} \\
${aligned} \\
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -64,15 +65,16 @@ process CENTRIFUGE_CENTRIFUGE {
"""

stub:
def args = task.ext.args ?: ''
def _args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def _paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def unaligned = ''
def aligned = ''
if (meta.single_end) {
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
} else {
}
else {
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
}
Expand Down
3 changes: 2 additions & 1 deletion modules/nf-core/centrifuge/kreport/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::centrifuge=1.0.4.1
- bioconda::centrifuge=1.0.4.2
17 changes: 10 additions & 7 deletions modules/nf-core/centrifuge/kreport/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
process CENTRIFUGE_KREPORT {
tag "$meta.id"
tag "${meta.id}"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
: 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"

input:
tuple val(meta), path(report)
path db

output:
tuple val(meta), path('*.txt'), emit: kreport
path "versions.yml" , emit: versions
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -23,7 +23,10 @@ process CENTRIFUGE_KREPORT {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/\\.1.cf\$//'`
centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
centrifuge-kreport \\
${args} \\
-x \$db_name \\
${report} > ${prefix}.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -32,7 +35,7 @@ process CENTRIFUGE_KREPORT {
"""

stub:
def args = task.ext.args ?: ''
def _args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.txt
Expand Down
Loading