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Change sed regex for version reporting in pigz modules #6878

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Change sed regex for version reporting in pigz modules #6878

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75af334
added missing backslash in pigz uncompress stub
ljwharbers Oct 28, 2024
d51be89
changed sed regex for both pigz/uncompress and pigz/compress
ljwharbers Oct 30, 2024
c6dae48
Merge branch 'master' into master
fellen31 Oct 30, 2024
f4cea01
fixed stub, added stub test and updated snap
ljwharbers Oct 30, 2024
4719a57
merge with main branch 'master' of https://github.com/ljwharbers/modules
ljwharbers Oct 30, 2024
5601c1a
Merge branch 'master' into master
ljwharbers Oct 30, 2024
50367a4
Update modules/nf-core/pigz/uncompress/tests/main.nf.test
ljwharbers Oct 30, 2024
d7dabe2
fixed linting
ljwharbers Oct 30, 2024
00ccdaa
added types to input
ljwharbers Oct 30, 2024
a2a6189
updated snap
ljwharbers Oct 30, 2024
8507a36
revert linting changes of tcoffee/irmsd
ljwharbers Oct 30, 2024
0e40a6f
added types and description to fix linting issues in tcoffee/irmsd
ljwharbers Oct 30, 2024
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4 changes: 2 additions & 2 deletions modules/nf-core/pigz/compress/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ process PIGZ_COMPRESS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz:\$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )
pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
END_VERSIONS
"""

Expand All @@ -39,7 +39,7 @@ process PIGZ_COMPRESS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz:\$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )
pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
END_VERSIONS
"""
}
6 changes: 3 additions & 3 deletions modules/nf-core/pigz/uncompress/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -30,19 +30,19 @@ process PIGZ_UNCOMPRESS {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
uncompressed_filename = zip.toString() - '.gz'
"""
touch ${zip.dropRight(3)}
touch $uncompressed_filename

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\w*//' ))
pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz[[:space:]]*//' )
END_VERSIONS
"""
}
25 changes: 25 additions & 0 deletions modules/nf-core/pigz/uncompress/tests/main.nf.test
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Expand Up @@ -29,5 +29,30 @@ nextflow_process {
}

}

test("Should run without failures - stub") {

options "-stub"

when {
params {
outdir = "$outputDir"
}
process {
"""
input[0] = [ [ id:'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

}
43 changes: 38 additions & 5 deletions modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,37 @@
{
"Should run without failures - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
],
"file": [
[
{
"id": "test"
},
"test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-30T14:42:44.906844906"
},
"Should run without failures": {
"content": [
{
Expand All @@ -11,7 +44,7 @@
]
],
"1": [
"versions.yml:md5,a2d5ce72baa8b303f25afb9cf094f683"
"versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
],
"file": [
[
Expand All @@ -22,14 +55,14 @@
]
],
"versions": [
"versions.yml:md5,a2d5ce72baa8b303f25afb9cf094f683"
"versions.yml:md5,e0c776f8d0bfa6d8e49e02aeb0728355"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.03.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-15T16:43:21.55056643"
"timestamp": "2024-10-30T10:58:22.006893497"
}
}
9 changes: 9 additions & 0 deletions modules/nf-core/tcoffee/irmsd/meta.yml
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Expand Up @@ -26,11 +26,20 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', ... ]
- msa:
type: file
description: File containing the multiple sequence alignment
- - meta2:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- template:
type: file
description: File containing the template structure
- structures:
type: file
description: File containing the structures
output:
- irmsd:
- meta:
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