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Topics for a bunch of SV related modules (nf-core#10113)
* topics delly/call * topic smoove/call * topics strvctvre/strvctvre * topics svtools/vcftobedpe * topics svync * topics wisecondorx/gender * topics wisecondorx/convert * topics wisecondorx/newref * topics wisecondorx/predict * fix bam_cnv_wisecondorx
1 parent eb57b95 commit fdcc397

39 files changed

Lines changed: 501 additions & 658 deletions

‎modules/nf-core/delly/call/main.nf‎

Lines changed: 1 addition & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@ process DELLY_CALL {
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output:
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tuple val(meta), path("*.{bcf,vcf.gz}") , emit: bcf
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tuple val(meta), path("*.{csi,tbi}") , emit: csi
18-
path "versions.yml" , emit: versions
18+
tuple val("${task.process}"), val('delly'), eval("delly --version |& sed -n '1s/Delly version: *v//p'"), emit: versions_delly, topic: versions
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2020
when:
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task.ext.when == null || task.ext.when
@@ -43,11 +43,6 @@ process DELLY_CALL {
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${exclude} \\
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${input} \\
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${vcf_output}
46-
47-
cat <<-END_VERSIONS > versions.yml
48-
"${task.process}":
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delly: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//')
50-
END_VERSIONS
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"""
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stub:
@@ -60,10 +55,5 @@ process DELLY_CALL {
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"""
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${bcf_output}
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${vcf_output}
63-
64-
cat <<-END_VERSIONS > versions.yml
65-
"${task.process}":
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delly: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//')
67-
END_VERSIONS
6858
"""
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}

‎modules/nf-core/delly/call/meta.yml‎

Lines changed: 34 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -7,12 +7,13 @@ keywords:
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- bcf
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tools:
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- delly:
10-
description: Structural variant discovery by integrated paired-end and split-read
11-
analysis
10+
description: Structural variant discovery by integrated paired-end and
11+
split-read analysis
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homepage: https://github.com/dellytools/delly
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documentation: https://github.com/dellytools/delly/blob/master/README.md
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doi: "10.1093/bioinformatics/bts378"
15-
licence: ["BSD-3-Clause"]
15+
licence:
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- "BSD-3-Clause"
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identifier: ""
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input:
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- - meta:
@@ -22,8 +23,8 @@ input:
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e.g. [ id:'test', single_end:false ]
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- input:
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type: file
25-
description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate
26-
marked
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description: BAM/CRAM file from alignment must be sorted, indexed, and
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duplicate marked
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pattern: "*.{bam,cram}"
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ontologies: []
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- input_index:
@@ -33,8 +34,8 @@ input:
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ontologies: []
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- vcf:
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type: file
36-
description: A BCF/VCF file to genotype with Delly. If this is supplied, the
37-
variant calling will be skipped
37+
description: A BCF/VCF file to genotype with Delly. If this is supplied,
38+
the variant calling will be skipped
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pattern: "*.{vcf.gz,bcf}"
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ontologies: []
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- vcf_index:
@@ -44,8 +45,8 @@ input:
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ontologies: []
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- exclude_bed:
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type: file
47-
description: An optional bed file containing regions to exclude from the called
48-
VCF
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description: An optional bed file containing regions to exclude from the
49+
called VCF
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pattern: "*.bed"
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ontologies: []
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- - meta2:
@@ -77,8 +78,8 @@ output:
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e.g. [ id:'test', single_end:false ]
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- "*.{bcf,vcf.gz}":
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type: file
80-
description: Called variants in BCF/VCF format. Specify either "bcf" or "vcf"
81-
in ext.suffix to define the output type
81+
description: Called variants in BCF/VCF format. Specify either "bcf" or
82+
"vcf" in ext.suffix to define the output type
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pattern: "*.{bcf,vcf.gz}"
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ontologies: []
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csi:
@@ -89,17 +90,31 @@ output:
8990
e.g. [ id:'test', single_end:false ]
9091
- "*.{csi,tbi}":
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type: file
92-
description: A generated csi index that matches the bcf output (not generated
93-
for vcf files)
93+
description: A generated csi index that matches the bcf output (not
94+
generated for vcf files)
9495
pattern: "*.{bcf.csi}"
9596
ontologies: []
97+
versions_delly:
98+
- - ${task.process}:
99+
type: string
100+
description: The name of the process
101+
- delly:
102+
type: string
103+
description: The name of the tool
104+
- "delly --version |& sed -n '1s/Delly version: *v//p'":
105+
type: eval
106+
description: The expression to obtain the version of the tool
107+
topics:
96108
versions:
97-
- versions.yml:
98-
type: file
99-
description: File containing software versions
100-
pattern: "versions.yml"
101-
ontologies:
102-
- edam: http://edamontology.org/format_3750 # YAML
109+
- - ${task.process}:
110+
type: string
111+
description: The name of the process
112+
- delly:
113+
type: string
114+
description: The name of the tool
115+
- "delly --version |& sed -n '1s/Delly version: *v//p'":
116+
type: eval
117+
description: The expression to obtain the version of the tool
103118
authors:
104119
- "@projectoriented"
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- "@nvnieuwk"

‎modules/nf-core/delly/call/tests/main.nf.test‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ nextflow_process {
3939
then {
4040
assertAll(
4141
{ assert process.success },
42-
{ assert snapshot(process.out).match("bam") }
42+
{ assert snapshot(sanitizeOutput(process.out)).match() }
4343
)
4444
}
4545

@@ -73,7 +73,7 @@ nextflow_process {
7373
then {
7474
assertAll(
7575
{ assert process.success },
76-
{ assert snapshot(process.out).match("cram") }
76+
{ assert snapshot(sanitizeOutput(process.out)).match() }
7777
)
7878
}
7979

@@ -107,7 +107,7 @@ nextflow_process {
107107
then {
108108
assertAll(
109109
{ assert process.success },
110-
{ assert snapshot(process.out).match("bed") }
110+
{ assert snapshot(sanitizeOutput(process.out)).match() }
111111
)
112112
}
113113

@@ -141,7 +141,7 @@ nextflow_process {
141141
then {
142142
assertAll(
143143
{ assert process.success },
144-
{ assert snapshot(process.out).match("genotype") }
144+
{ assert snapshot(sanitizeOutput(process.out)).match() }
145145
)
146146
}
147147

@@ -178,7 +178,7 @@ nextflow_process {
178178
then {
179179
assertAll(
180180
{ assert process.success },
181-
{ assert snapshot(process.out).match("stub") }
181+
{ assert snapshot(sanitizeOutput(process.out)).match() }
182182
)
183183
}
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