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Update bcftools query #3605

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merged 13 commits into from
Jul 6, 2023
Merged

Update bcftools query #3605

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8df2221
new module picard/scatterintervalsbyns
nvnieuwk Jun 1, 2023
3780c6c
update annotsv to 3.3.6
nvnieuwk Jun 2, 2023
4a4979c
Merge branch 'master' into annotsv-update
nvnieuwk Jun 2, 2023
5533a7e
update installannotations
nvnieuwk Jun 2, 2023
0b8330f
Merge branch 'annotsv-update' of github.com:nvnieuwk/modules into ann…
nvnieuwk Jun 2, 2023
f772c25
Merge branch 'nf-core:master' into master
nvnieuwk Jun 5, 2023
d84dc41
Merge branch 'nf-core:master' into master
nvnieuwk Jun 20, 2023
f980e00
Merge branch 'nf-core:master' into master
nvnieuwk Jun 20, 2023
e82b71c
Merge branch 'nf-core:master' into master
nvnieuwk Jun 29, 2023
289314b
Merge branch 'nf-core:master' into master
nvnieuwk Jun 29, 2023
eb7ca02
Merge branch 'nf-core:master' into master
nvnieuwk Jun 29, 2023
a228da4
Merge branch 'nf-core:master' into master
nvnieuwk Jul 6, 2023
81e395c
update output of bcftools query
nvnieuwk Jul 6, 2023
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10 changes: 6 additions & 4 deletions modules/nf-core/bcftools/query/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,15 +14,16 @@ process BCFTOOLS_QUERY {
path samples

output:
tuple val(meta), path("*.txt"), emit: txt
path "versions.yml" , emit: versions
tuple val(meta), path("*.${suffix}"), emit: output
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}"
suffix = task.ext.suffix ?: "txt"
def regions_file = regions ? "--regions-file ${regions}" : ""
def targets_file = targets ? "--targets-file ${targets}" : ""
def samples_file = samples ? "--samples-file ${samples}" : ""
Expand All @@ -33,7 +34,7 @@ process BCFTOOLS_QUERY {
$samples_file \\
$args \\
$vcf \\
> ${prefix}.txt
> ${prefix}.${suffix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -43,8 +44,9 @@ process BCFTOOLS_QUERY {

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
suffix = task.ext.suffix ?: "txt"
"""
touch ${prefix}.txt \\
touch ${prefix}.${suffix} \\

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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3 changes: 1 addition & 2 deletions modules/nf-core/bcftools/query/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -48,10 +48,9 @@ output:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- txt:
- output:
type: file
description: BCFTools query output file
pattern: "*.txt"
- versions:
type: file
description: File containing software versions
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4 changes: 2 additions & 2 deletions tests/modules/nf-core/bcftools/query/test.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
- name: bcftools query test_bcftools_query
command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
tags:
- bcftools
- bcftools/query
- bcftools
files:
- path: output/bcftools/out.txt
md5sum: 51d135de052f3bcef50dcd6b74806094
Expand All @@ -11,8 +11,8 @@
- name: bcftools query test_bcftools_query_with_optional_files
command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
tags:
- bcftools
- bcftools/query
- bcftools
files:
- path: output/bcftools/out.txt
md5sum: 1785d1957ba7206df852d0689b91753f
Expand Down