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Remove langage server warnings #6937

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Remove langage server warnings #6937

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e2721f0
first modules from Sarek
maxulysse Nov 5, 2024
1a4b05e
Merge branch 'master' into sarek_language_server
SPPearce Nov 8, 2024
2db56a2
Merge branch 'master' into sarek_language_server
SPPearce Nov 26, 2024
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12 changes: 6 additions & 6 deletions modules/nf-core/bcftools/mpileup/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,9 @@ process BCFTOOLS_MPILEUP {
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
def bgzip_mpileup = save_mpileup ? "bgzip ${prefix}.mpileup" : ""
def intervals = intervals ? "-T ${intervals}" : ""
def mpileup_command = save_mpileup ? "| tee ${prefix}.mpileup" : ""
def bgzip_command = save_mpileup ? "bgzip ${prefix}.mpileup" : ""
def intervals_command = intervals ? "-T ${intervals}" : ""
"""
echo "${meta.id}" > sample_name.list

Expand All @@ -38,13 +38,13 @@ process BCFTOOLS_MPILEUP {
--fasta-ref $fasta \\
$args \\
$bam \\
$intervals \\
$mpileup \\
$intervals_command \\
$mpileup_command \\
| bcftools call --output-type v $args2 \\
| bcftools reheader --samples sample_name.list \\
| bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3

$bgzip_mpileup
$bgzip_command

tabix -p vcf -f ${prefix}.vcf.gz

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2 changes: 1 addition & 1 deletion modules/nf-core/bwa/index/main.nf
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Expand Up @@ -12,7 +12,7 @@ process BWA_INDEX {

output:
tuple val(meta), path("bwa") , emit: index
path "versions.yml" , emit: versions
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down
49 changes: 27 additions & 22 deletions modules/nf-core/bwamem2/mem/main.nf
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Original file line number Diff line number Diff line change
@@ -1,25 +1,24 @@
process BWAMEM2_MEM {
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-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' :
'biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0'
: 'biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0'}"

input:
tuple val(meta), path(reads)
tuple val(meta2), path(index)
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
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
Comment on lines +16 to +20
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Why has this gone all wibbly-wobbly?

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You need to turn on the Harshil Alignment in the settings. I'll make a PR for the workspace.

path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -31,21 +30,23 @@ process BWAMEM2_MEM {
def samtools_command = sort_bam ? 'sort' : 'view'

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"
def reference = fasta && extension=="cram" ? "--reference ${fasta}" : ""
if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
def reference = fasta && extension == "cram" ? "--reference ${fasta}" : ""
if (!fasta && extension == "cram") {
error("Fasta reference is required for CRAM output")
}

"""
INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`

bwa-mem2 \\
mem \\
$args \\
-t $task.cpus \\
${args} \\
-t ${task.cpus} \\
\$INDEX \\
$reads \\
| samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} -
${reads} \\
| samtools ${samtools_command} ${args2} -@ ${task.cpus} ${reference} -o ${prefix}.${extension} -

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -59,14 +60,18 @@ process BWAMEM2_MEM {
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${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"
}

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