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Fix bcftools stubs to behave like program #6666

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Fix bcftools stubs to behave like program #6666

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39 changes: 24 additions & 15 deletions modules/nf-core/bcftools/annotate/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,7 @@ process BCFTOOLS_ANNOTATE {
def prefix = task.ext.prefix ?: "${meta.id}"
def header_file = header_lines ? "--header-lines ${header_lines}" : ''
def annotations_file = annotations ? "--annotations ${annotations}" : ''
def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"
def extension = getVcfExtension(args);
def index_command = !index ? "bcftools index $input" : ''

if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
Expand All @@ -54,18 +50,12 @@ process BCFTOOLS_ANNOTATE {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"
def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
args.contains("--write-index") || args.contains("-W") ? "csi" :
""
def extension = getVcfExtension(args);
def index = getVcfIndex(args, extension);
def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""

if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
${create_cmd} ${prefix}.${extension}
${create_index}
Expand All @@ -76,3 +66,22 @@ process BCFTOOLS_ANNOTATE {
END_VERSIONS
"""
}
// Custom Functions
String getVcfExtension(String args) {
return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf";
}
String getVcfIndex(String args, String extension) {
index = ''
if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') {
index = 'tbi'
} else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
index = 'csi'
}
}
return index
}
21 changes: 15 additions & 6 deletions modules/nf-core/bcftools/call/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -47,12 +47,9 @@ process BCFTOOLS_CALL {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
args.contains("--write-index") || args.contains("-W") ? "csi" :
""

def create_index = index.matches("csi|tbi") ? "touch ${prefix}.vcf.gz.${index}" : ""
def extension = "vcf.gz"
def index = getVcfIndex(args, extension);
def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""

"""
echo "" | gzip > ${prefix}.vcf.gz
Expand All @@ -64,3 +61,15 @@ process BCFTOOLS_CALL {
END_VERSIONS
"""
}
// Custom Functions
String getVcfIndex(String args, String extension) {
index = ''
if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') {
index = 'tbi'
} else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
index = 'csi'
}
}
return index
}
19 changes: 14 additions & 5 deletions modules/nf-core/bcftools/concat/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,9 @@ process BCFTOOLS_CONCAT {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
args.contains("--write-index") || args.contains("-W") ? "csi" :
""
def create_index = index.matches("csi|tbi") ? "touch ${prefix}.vcf.gz.${index}" : ""
def extension = "vcf.gz"
def index = getVcfIndex(args, extension);
def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
"""
echo "" | gzip > ${prefix}.vcf.gz
${create_index}
Expand All @@ -53,3 +51,14 @@ process BCFTOOLS_CONCAT {
END_VERSIONS
"""
}
String getVcfIndex(String args, String extension) {
index = ''
if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') {
index = 'tbi'
} else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
index = 'csi'
}
}
return index
}
40 changes: 27 additions & 13 deletions modules/nf-core/bcftools/convert/main.nf
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Expand Up @@ -31,18 +31,13 @@ process BCFTOOLS_CONVERT {

def regions = bed ? "--regions-file $bed" : ""
def reference = fasta ? "--fasta-ref $fasta" : ""
def extension = args.contains("--output-type b") || args.contains("-Ob") ? "--output ${prefix}.bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "--output ${prefix}.bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "--output ${prefix}.vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "--output ${prefix}.vcf" :
args.contains("--haplegendsample") || args.contains("-h") ? "" :
"--output ${prefix}.vcf.gz"
def extension = getVcfExtension(args);

"""
bcftools convert \\
$args \\
$regions \\
$extension \\
--output ${prefix}.${extension} \\
--threads $task.cpus \\
$reference \\
$input
Expand All @@ -56,18 +51,37 @@ process BCFTOOLS_CONVERT {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def extension = getVcfExtension(args);
def index = getVcfIndex(args, extension);
def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""

def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf.gz"
"""
touch ${prefix}.${extension}
${create_cmd} ${prefix}.${extension}
${create_index}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}
// Custom Functions
String getVcfExtension(String args) {
return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf.gz";
}
String getVcfIndex(String args, String extension) {
index = ''
if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') {
index = 'tbi'
} else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
index = 'csi'
}
}
return index
}
19 changes: 14 additions & 5 deletions modules/nf-core/bcftools/csq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -51,20 +51,18 @@ process BCFTOOLS_CSQ {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
extension = getVcfExtension(args);
index = getVcfIndex(args, extension);

def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
args.contains("--write-index") || args.contains("-W") ? "csi" :
""
def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""

if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"

"""
${create_cmd} ${prefix}.${extension}
${create_index}


cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
Expand All @@ -79,3 +77,14 @@ String getVcfExtension(String args) {
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf";
}
String getVcfIndex(String args, String extension) {
index = ''
if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') {
index = 'tbi'
} else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
index = 'csi'
}
}
return index
}
38 changes: 23 additions & 15 deletions modules/nf-core/bcftools/filter/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,7 @@ process BCFTOOLS_FILTER {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"
extension = getVcfExtension(args);

if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"

Expand All @@ -47,17 +43,10 @@ process BCFTOOLS_FILTER {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"
def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
args.contains("--write-index") || args.contains("-W") ? "csi" :
""
extension = getVcfExtension(args);
def index = getVcfIndex(args, extension);
def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""

if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"

Expand All @@ -71,3 +60,22 @@ process BCFTOOLS_FILTER {
END_VERSIONS
"""
}
// Custom Functions
String getVcfExtension(String args) {
return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf";
}
String getVcfIndex(String args, String extension) {
index = ''
if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') {
index = 'tbi'
} else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
index = 'csi'
}
}
return index
}
8 changes: 5 additions & 3 deletions modules/nf-core/bcftools/index/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -38,10 +38,12 @@ process BCFTOOLS_INDEX {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def extension = args.contains("--tbi") || args.contains("-t") ? "tbi" :
"csi"
def index = (args.contains("--tbi") || args.contains("-t")) && vcf.endsWith("vcf.gz") ? "tbi" :
(args.contains("--csi") || args.contains("-c")) && !vcf.endsWith("vcf") ? "csi" :
""
def create_index = index ? "touch ${vcf}.${index}" : ""
"""
touch ${vcf}.${extension}
${create_index}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
39 changes: 23 additions & 16 deletions modules/nf-core/bcftools/merge/main.nf
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Expand Up @@ -27,11 +27,7 @@ process BCFTOOLS_MERGE {

def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs
def regions = bed ? "--regions-file $bed" : ""
def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"
def extension = getVcfExtension(args);

"""
bcftools merge \\
Expand All @@ -50,18 +46,10 @@ process BCFTOOLS_MERGE {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"
def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
args.contains("--write-index") || args.contains("-W") ? "csi" :
""
def extension = getVcfExtension(args);
def index = getVcfIndex(args, extension);
def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""

def create_index = index ? "touch ${prefix}.${extension}.${index}" : ""
"""
${create_cmd} ${prefix}.${extension}
${create_index}
Expand All @@ -72,3 +60,22 @@ process BCFTOOLS_MERGE {
END_VERSIONS
"""
}
// Custom Functions
String getVcfExtension(String args) {
return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf";
}
String getVcfIndex(String args, String extension) {
index = ''
if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) {
if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') {
index = 'tbi'
} else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) {
index = 'csi'
}
}
return index
}
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