From 79c863456d7e1ce6996847358462954c0f218c05 Mon Sep 17 00:00:00 2001 From: Edu Date: Tue, 15 Oct 2024 20:17:23 +0200 Subject: [PATCH 1/2] Updated containers to 2.7.1 that enables the pod5 file support --- modules/nf-core/toulligqc/environment.yml | 2 +- modules/nf-core/toulligqc/main.nf | 4 ++-- modules/nf-core/toulligqc/meta.yml | 1 + 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/toulligqc/environment.yml b/modules/nf-core/toulligqc/environment.yml index 2d160afe2da..a2049d263c0 100644 --- a/modules/nf-core/toulligqc/environment.yml +++ b/modules/nf-core/toulligqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::toulligqc=2.5.6" + - "bioconda::toulligqc=2.7.1" diff --git a/modules/nf-core/toulligqc/main.nf b/modules/nf-core/toulligqc/main.nf index 71ced04314f..c0ee87fcc5a 100644 --- a/modules/nf-core/toulligqc/main.nf +++ b/modules/nf-core/toulligqc/main.nf @@ -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: diff --git a/modules/nf-core/toulligqc/meta.yml b/modules/nf-core/toulligqc/meta.yml index b269eccf801..0409470be46 100644 --- a/modules/nf-core/toulligqc/meta.yml +++ b/modules/nf-core/toulligqc/meta.yml @@ -74,3 +74,4 @@ authors: - "@Salome-Brunon" maintainers: - "@Salome-Brunon" + - "@eperezme" From d2731040815c5dd23a213b583fd9b8d6776692be Mon Sep 17 00:00:00 2001 From: Edu Date: Tue, 10 Dec 2024 09:22:38 +0100 Subject: [PATCH 2/2] Run: nf-core modules test toulligqc -u --- .../nf-core/toulligqc/tests/main.nf.test.snap | 82 +++++++++++++------ 1 file changed, 59 insertions(+), 23 deletions(-) diff --git a/modules/nf-core/toulligqc/tests/main.nf.test.snap b/modules/nf-core/toulligqc/tests/main.nf.test.snap index 025c3c2badf..c6757f39bc7 100644 --- a/modules/nf-core/toulligqc/tests/main.nf.test.snap +++ b/modules/nf-core/toulligqc/tests/main.nf.test.snap @@ -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": [ @@ -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": [ @@ -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", @@ -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", @@ -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" } } \ No newline at end of file