Skip to content

Commit

Permalink
Add sylph/profile module (#7118)
Browse files Browse the repository at this point in the history 
* Add sylph/profile module and remove unnecessary pattern from sylph/sketch

* Remove description

* Update snap

* Try again with linting

* Update snap

* Fix linting for meta.yaml

* Update tests

* Add contains in nf-test

* Add contains

* Update modules/nf-core/sylph/profile/tests/main.nf.test

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/sylph/profile/main.nf

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/sylph/profile/main.nf

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/sylph/profile/main.nf

Co-authored-by: Famke Bäuerle <[email protected]>

* Update description

* Remove single_end from the output

* Update meta.yml file to include info if fastq/fasta files are provided

* Add tests

* Fix test

* Fix tests

* Update modules/nf-core/sylph/profile/tests/main.nf.test

Co-authored-by: Simon Pearce <[email protected]>

* Update modules/nf-core/sylph/profile/main.nf

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update to latest paths

* Rename variable to database

* Update modules/nf-core/sylph/profile/tests/main.nf.test

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/sylph/sketch/meta.yml

Co-authored-by: Famke Bäuerle <[email protected]>

* Apply review suggestions

* Update snap

* Snapshot

* Test snap

* Update snapshot to pass the tests

* Remove test_2.fastq.gz from single_end test

* Update modules/nf-core/sylph/profile/tests/main.nf.test

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/sylph/profile/tests/main.nf.test

Co-authored-by: Famke Bäuerle <[email protected]>

* Update snapshot

* Add threads

* Update modules/nf-core/sylph/profile/main.nf

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update modules/nf-core/sylph/profile/meta.yml

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update modules/nf-core/sylph/profile/tests/main.nf.test

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/sylph/profile/main.nf

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update modules/nf-core/sylph/profile/tests/main.nf.test

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/sylph/profile/main.nf

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* add better debugging

* Update tests

* Update snapshot

---------

Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
Co-authored-by: mashehu <[email protected]>
  • Loading branch information
@sofstam @mashehu
@famosab @SPPearce @mahesh-panchal
6 people authored Jan 30, 2025
1 parent 29a9928 commit cfe3660
Show file tree
Hide file tree
Showing 7 changed files with 256 additions and 8 deletions.
13 changes: 7 additions & 6 deletions .github/actions/get-shards/action.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@ outputs:
total_shards:
description: "Total number of shards"
value: ${{ steps.shards.outputs.total_shards }}

runs:
using: "composite"
steps:
Expand All @@ -26,22 +25,24 @@ runs:
with:
version: ${{ env.NFT_VER }}
install-pdiff: true

- name: Get number of shards
id: shards
shell: bash
run: |
# Prepare tag parameter if tags are provided
TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
# Run nf-test with dynamic tag parameter
# Run nf-test with dynamic parameter
nftest_output=$(nf-test test \
--dry-run \
--profile docker \
${TAGS} \
--filter process,workflow \
${{ inputs.paths }})
${{ inputs.paths }}) || {
echo "nf-test command failed with exit code $?"
echo "Full output: $nftest_output"
exit 1
}
echo "nf-test dry-run output: $nftest_output"
# Default values for shard and total_shards
Expand Down
7 changes: 7 additions & 0 deletions modules/nf-core/sylph/profile/environment.yml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::sylph=0.7.0"
49 changes: 49 additions & 0 deletions modules/nf-core/sylph/profile/main.nf
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
process SYLPH_PROFILE {
tag "$meta.id"
label 'process_high'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sylph:0.7.0--h919a2d8_0' :
'biocontainers/sylph:0.7.0--h919a2d8_0' }"

input:
tuple val(meta), path(reads)
path(database)

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

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
sylph profile \\
-t $task.cpus \\
$args \\
$reads \\
$database\\
-o ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
sylph: \$(sylph -V | awk '{print \$2}')
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
sylph: \$(sylph -V | awk '{print \$2}')
END_VERSIONS
"""

}
51 changes: 51 additions & 0 deletions modules/nf-core/sylph/profile/meta.yml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
name: "sylph_profile"
description: Sylph profile command for taxonoming profiling
keywords:
- profile
- metagenomics
- sylph
- classification
tools:
- sylph:
description: Sylph quickly enables querying of genomes against even low-coverage
shotgun metagenomes to find nearest neighbour ANI.
homepage: https://github.com/bluenote-1577/sylph
documentation: https://github.com/bluenote-1577/sylph
tool_dev_url: https://github.com/bluenote-1577/sylph
doi: 10.1038/s41587-024-02412-y
licence: ["MIT"]
identifier: biotools:sylph
input:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
- reads:
type: file
description: |
List of input FastQ/FASTA files of size 1 and 2 for single-end and paired-end data,
respectively. They are automatically sketched to .sylsp/.syldb
- - database:
type: file
description: Pre-sketched *.syldb/*.sylsp files. Raw single-end fastq/fasta are allowed and will be automatically sketched to .sylsp/.syldb.
pattern: "*.{syldb,sylsp,fasta,fastq}"
output:
- profile_out:
- meta:
type: map
description: Groovy Map containing sample information
- "*.tsv":
type: file
description: Output file of species-level taxonomic profiling with abundances and ANIs.
pattern: "*tsv"
- versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@jiahang1234"
- "@sofstam"
maintainers:
- "@sofstam"
80 changes: 80 additions & 0 deletions modules/nf-core/sylph/profile/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,80 @@
nextflow_process {

name "Test Process SYLPH_PROFILE"
script "../main.nf"
process "SYLPH_PROFILE"
tag "modules"
tag "modules_nfcore"
tag "sylph"
tag "sylph/profile"

test("sarscov2 illumina single-end [fastq_gz]") {
when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
]
]
input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
}
}

then {
assert process.success
assert snapshot(
process.out.versions,
file(process.out.profile_out[0][1]).readLines()[0]
).match()
}
}

test("sarscov2 illumina paired-end [fastq_gz]") {
when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
]
]
input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
}
}

then {
assert process.success
assert snapshot(
process.out.versions,
file(process.out.profile_out[0][1]).readLines()[0]
).match()
}
}

test("sarscov2 illumina paired-end [fastq_gz]-stub") {
options "-stub"

when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
]
]
input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
}
}

then {
assert process.success
assert snapshot(process.out).match()
}
}
}
61 changes: 61 additions & 0 deletions modules/nf-core/sylph/profile/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
{
"sarscov2 illumina paired-end [fastq_gz]": {
"content": [
[
"versions.yml:md5,7b5a545483277cc0ff9189f8891e737f"
],
"Sample_file\tGenome_file\tTaxonomic_abundance\tSequence_abundance\tAdjusted_ANI\tEff_cov\tANI_5-95_percentile\tEff_lambda\tLambda_5-95_percentile\tMedian_cov\tMean_cov_geq1\tContainment_ind\tNaive_ANI\tkmers_reassigned\tContig_name"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-27T15:47:59.374481624"
},
"sarscov2 illumina single-end [fastq_gz]": {
"content": [
[
"versions.yml:md5,7b5a545483277cc0ff9189f8891e737f"
],
"Sample_file\tGenome_file\tTaxonomic_abundance\tSequence_abundance\tAdjusted_ANI\tEff_cov\tANI_5-95_percentile\tEff_lambda\tLambda_5-95_percentile\tMedian_cov\tMean_cov_geq1\tContainment_ind\tNaive_ANI\tkmers_reassigned\tContig_name"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-27T15:47:53.556942841"
},
"sarscov2 illumina paired-end [fastq_gz]-stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,7b5a545483277cc0ff9189f8891e737f"
],
"profile_out": [
[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,7b5a545483277cc0ff9189f8891e737f"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-27T15:48:04.991824868"
}
}
3 changes: 1 addition & 2 deletions modules/nf-core/sylph/sketch/meta.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,7 @@ output:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
pattern: "my_sketches/*.sylsp"
e.g. [ id:'test']
- my_sketches/*.sylsp:
type: map
description: |
Expand Down

0 comments on commit cfe3660

Please sign in to comment.