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Update toulligqc to 2.7.1 #6786

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Update toulligqc to 2.7.1 #6786

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79c8634
Updated containers to 2.7.1 that enables the pod5 file support
eperezme Oct 15, 2024
d273104
Run:
eperezme Dec 10, 2024
d5f879b
Merge branch 'master' into toulligqc
famosab Dec 10, 2024
22207e0
Merge branch 'master' into toulligqc
sateeshperi Dec 10, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/toulligqc/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::toulligqc=2.5.6"
- "bioconda::toulligqc=2.7.1"
4 changes: 2 additions & 2 deletions modules/nf-core/toulligqc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process TOULLIGQC {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/toulligqc:2.5.6--pyhdfd78af_0':
'biocontainers/toulligqc:2.5.6--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/toulligqc:2.7.1--pyhdfd78af_0':
'biocontainers/toulligqc:2.7.1--pyhdfd78af_0' }"

input:

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1 change: 1 addition & 0 deletions modules/nf-core/toulligqc/meta.yml
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I have also noticed that here in the meta there is groovy maps mentioned sith single_end information. Which is probably not applicable to that kind of data. Could you remove these if thats the case? Everything else looks good to go :)

Original file line number Diff line number Diff line change
Expand Up @@ -74,3 +74,4 @@ authors:
- "@Salome-Brunon"
maintainers:
- "@Salome-Brunon"
- "@eperezme"
82 changes: 59 additions & 23 deletions modules/nf-core/toulligqc/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -68,15 +68,23 @@
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.max=nan"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-02T16:00:29.481355"
},
"toulligqc_versions_sequencing_summary_barcodes": {
"content": [
[
"versions.yml:md5,3be42e94e756b5a89167a891d287c538"
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
],
"timestamp": "2024-05-02T16:00:41.607538"
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-12-10T09:18:53.88156"
},
"sarscov2 - nanopore sequencing_summary + barcodes": {
"content": [
Expand Down Expand Up @@ -147,15 +155,23 @@
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.75%=nan"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-02T16:00:41.63299"
},
"toulligqc_versions_bam": {
"content": [
[
"versions.yml:md5,3be42e94e756b5a89167a891d287c538"
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
],
"timestamp": "2024-05-02T16:01:05.074867"
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-12-10T09:19:22.5334"
},
"sarscov2 - nanopore bam": {
"content": [
Expand Down Expand Up @@ -226,37 +242,53 @@
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.max=18.110000610351562"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-02T16:01:05.091838"
},
"toulligqc_versions_stub": {
"content": [
[
"versions.yml:md5,3be42e94e756b5a89167a891d287c538"
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
],
"timestamp": "2024-05-02T16:01:12.876406"
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-12-10T09:19:32.786683"
},
"toulligqc_versions_fastq": {
"content": [
[
"versions.yml:md5,3be42e94e756b5a89167a891d287c538"
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
],
"timestamp": "2024-05-02T16:00:52.810853"
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-12-10T09:19:08.163453"
},
"toulligqc_versions_sequencing_summary": {
"content": [
[
"versions.yml:md5,3be42e94e756b5a89167a891d287c538"
"versions.yml:md5,cf868ab645663c8e30396b733d9fdd30"
]
],
"timestamp": "2024-05-02T16:00:29.458805"
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-12-10T09:18:39.743434"
},
"sarscov2 - nanopore fastq": {
"content": [
[
"sequencing.telemetry.extractor.run.id=Unknow",
"sequencing.telemetry.extractor.sample.id=Unknow",
"sequencing.telemetry.extractor.run.id=97ca62ca093ff43533aa34c38a10b1d6325e7e7b",
"sequencing.telemetry.extractor.sample.id=RN20097",
"sequencing.telemetry.extractor.model.file=Unknow",
"basecaller.sequencing.summary.1d.extractor.read.count=100",
"basecaller.sequencing.summary.1d.extractor.read.pass.count=96",
Expand All @@ -269,6 +301,15 @@
"basecaller.sequencing.summary.1d.extractor.yield=38253",
"basecaller.sequencing.summary.1d.extractor.n50=365",
"basecaller.sequencing.summary.1d.extractor.l50=67",
"basecaller.sequencing.summary.1d.extractor.run.time=2035.0",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.count=85.0",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.mean=1.1764705882352942",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.std=0.4412231534591759",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.min=1.0",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.25%=1.0",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.50%=1.0",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.75%=1.0",
"basecaller.sequencing.summary.1d.extractor.channel.occupancy.statistics.max=3.0",
"basecaller.sequencing.summary.1d.extractor.all.read.length.count=100.0",
"basecaller.sequencing.summary.1d.extractor.all.read.length.mean=382.53",
"basecaller.sequencing.summary.1d.extractor.all.read.length.std=219.37479828187222",
Expand Down Expand Up @@ -302,18 +343,13 @@
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.std=1.737709403038025",
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.min=9.84000015258789",
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.25%=11.90749979019165",
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.50%=12.820000171661377",
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.75%=14.09500002861023",
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.max=18.110000610351562",
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.mean=8.607500076293945",
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.std=0.27219802141189575",
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.min=8.199999809265137",
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.25%=8.59000015258789",
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.50%=8.735000133514404",
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.75%=8.752500057220459",
"basecaller.sequencing.summary.1d.extractor.fail.reads.mean.qscore.max=8.760000228881836"
"basecaller.sequencing.summary.1d.extractor.pass.reads.mean.qscore.50%=12.820000171661377"
]
],
"timestamp": "2024-05-02T16:00:52.831534"
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-12-10T09:19:08.233722"
}
}
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