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Merged
maxulysse merged 14 commits into from
Apr 10, 2025
Merged

Downgrade dragmap to the previous functionning version #8263

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42860a0
snapshot versions
maxulysse Apr 10, 2025
9e2d066
downgrade dragmap to a working version
maxulysse Apr 10, 2025
ac7adb8
Merge branch 'master' into dragmap_versions
maxulysse Apr 10, 2025
d15c455
update tests and snapshots
maxulysse Apr 10, 2025
75a2019
improve tests + fix environment.yml
maxulysse Apr 10, 2025
c5abcca
Merge branch 'master' into dragmap_versions
maxulysse Apr 10, 2025
cb88253
cursor :shakefist:
maxulysse Apr 10, 2025
b29c65b
same warning text
maxulysse Apr 10, 2025
d079971
fix linting
maxulysse Apr 10, 2025
cf01ad2
fix versions in environment.yml
maxulysse Apr 10, 2025
99d8ca2
update snapshots
maxulysse Apr 10, 2025
9e2309d
channels
maxulysse Apr 10, 2025
e18059e
Merge branch 'master' into dragmap_versions
maxulysse Apr 10, 2025
6eac144
Merge branch 'master' into dragmap_versions
maxulysse Apr 10, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/dragmap/align/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
channels:
- conda-forge
- bioconda

dependencies:
# WARN: Do not update this file to use 1.3.0 cf https://github.com/Illumina/DRAGMAP/issues/47
- dragmap=1.3.0
- pigz=2.8
- samtools=1.18
62 changes: 34 additions & 28 deletions modules/nf-core/dragmap/align/main.nf
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Original file line number Diff line number Diff line change
@@ -1,26 +1,27 @@
process DRAGMAP_ALIGN {
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/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:7eed251370ac7f3537c3d9472cdb2f9f5d8da1c5-0':
'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:7eed251370ac7f3537c3d9472cdb2f9f5d8da1c5-0' }"
// WARN: Do not update this file to use 1.3.0 cf https://github.com/Illumina/DRAGMAP/issues/47
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:df80ed8d23d0a2c43181a2b3dd1b39f2d00fab5c-0'
: 'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:df80ed8d23d0a2c43181a2b3dd1b39f2d00fab5c-0'}"

input:
tuple val(meta) , path(reads)
tuple val(meta), path(reads)
tuple val(meta2), path(hashmap)
tuple val(meta3), path(fasta)
val sort_bam
val sort_bam

output:
tuple val(meta), path("*.sam") , emit: sam , optional: true
tuple val(meta), path("*.bam") , emit: bam , optional: true
tuple val(meta), path("*.cram") , emit: cram , optional: true
tuple val(meta), path("*.crai") , emit: crai , optional: true
tuple val(meta), path("*.csi") , emit: csi , optional: true
tuple val(meta), path('*.log') , emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*.sam"), emit: sam, optional: true
tuple val(meta), path("*.bam"), emit: bam, optional: true
tuple val(meta), path("*.cram"), emit: cram, optional: true
tuple val(meta), path("*.crai"), emit: crai, optional: true
tuple val(meta), path("*.csi"), emit: csi, optional: true
tuple val(meta), path('*.log'), emit: log
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -29,22 +30,24 @@ process DRAGMAP_ALIGN {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
def samtools_command = sort_bam ? 'sort' : 'view'
def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
def extension_matcher = (args2 =~ extension_pattern)
def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
def reference = fasta && extension=="cram" ? "--reference ${fasta}" : ""
if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
def reads_command = meta.single_end ? "-1 ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def samtools_command = sort_bam ? 'sort' : 'view'
def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
def extension_matcher = (args2 =~ extension_pattern)
def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
def reference = fasta && extension == "cram" ? "--reference ${fasta}" : ""
if (!fasta && extension == "cram") {
error("Fasta reference is required for CRAM output")
}

"""
dragen-os \\
-r $hashmap \\
$args \\
--num-threads $task.cpus \\
$reads_command \\
-r ${hashmap} \\
${args} \\
--num-threads ${task.cpus} \\
${reads_command} \\
2> >(tee ${prefix}.dragmap.log >&2) \\
| samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -
| samtools ${samtools_command} ${args2} --threads ${task.cpus} ${reference} -o ${prefix}.${extension} -

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -58,14 +61,17 @@ process DRAGMAP_ALIGN {
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
def extension_matcher = (args2 =~ extension_pattern)
def extension_matcher = (args2 =~ extension_pattern)
def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
if (!fasta && extension == "cram") {
error("Fasta reference is required for CRAM output")
}

def create_index = ""
if (extension == "cram") {
create_index = "touch ${prefix}.crai"
} else if (extension == "bam") {
}
else if (extension == "bam") {
create_index = "touch ${prefix}.csi"
}

Expand Down
32 changes: 16 additions & 16 deletions modules/nf-core/dragmap/align/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -40,12 +40,12 @@ nextflow_process {
}

then {
assert { process.success }
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
file(process.out.versions[0]).name
path(process.out.versions[0]).yaml
).match() }
)
}
Expand Down Expand Up @@ -83,12 +83,13 @@ nextflow_process {
}

then {
assert { process.success }
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
file(process.out.versions[0]).name
path(process.out.versions[0]).yaml

).match() }
)
}
Expand Down Expand Up @@ -129,12 +130,13 @@ nextflow_process {
}

then {
assert { process.success }
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
file(process.out.versions[0]).name
path(process.out.versions[0]).yaml

).match() }
)
}
Expand Down Expand Up @@ -175,12 +177,13 @@ nextflow_process {
}

then {
assert { process.success }
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
file(process.out.versions[0]).name
path(process.out.versions[0]).yaml

).match() }
)
}
Expand Down Expand Up @@ -221,12 +224,12 @@ nextflow_process {
}

then {
assert { process.success }
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
file(process.out.versions[0]).name
path(process.out.versions[0]).yaml
).match() }
)
}
Expand Down Expand Up @@ -268,16 +271,13 @@ nextflow_process {
}

then {
assert { process.success }
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).name,
file(process.out.versions[0]).name
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}

}

}
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