From 60a3ace0cff7bbc42b2aaca0843139c08e5eb950 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Mon, 11 Nov 2024 11:55:58 -0800 Subject: [PATCH 1/4] chore: update fgbio version --- .../nf-core/fgbio/callduplexconsensusreads/environment.yml | 2 +- .../nf-core/fgbio/callmolecularconsensusreads/environment.yml | 2 +- modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml | 4 ++-- modules/nf-core/fgbio/fastqtobam/environment.yml | 2 +- modules/nf-core/fgbio/filterconsensusreads/environment.yml | 2 +- modules/nf-core/fgbio/groupreadsbyumi/environment.yml | 2 +- modules/nf-core/fgbio/sortbam/environment.yml | 2 +- modules/nf-core/fgbio/zipperbams/environment.yml | 2 +- 8 files changed, 9 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml b/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml index 6f3c75600d8..e2c4b144f32 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fgbio=2.2.1 + - bioconda::fgbio=2.4.0 diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml index 6f3c75600d8..e2c4b144f32 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fgbio=2.2.1 + - bioconda::fgbio=2.4.0 diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml index 48539f033bc..aa73390d8fa 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fgbio=2.0.2" - - "conda-forge::r-ggplot2=3.4.4" + - "bioconda::fgbio=2.4.0" + - "conda-forge::r-ggplot2=3.5.1" diff --git a/modules/nf-core/fgbio/fastqtobam/environment.yml b/modules/nf-core/fgbio/fastqtobam/environment.yml index 6f3c75600d8..e2c4b144f32 100644 --- a/modules/nf-core/fgbio/fastqtobam/environment.yml +++ b/modules/nf-core/fgbio/fastqtobam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fgbio=2.2.1 + - bioconda::fgbio=2.4.0 diff --git a/modules/nf-core/fgbio/filterconsensusreads/environment.yml b/modules/nf-core/fgbio/filterconsensusreads/environment.yml index 6f3c75600d8..e2c4b144f32 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/filterconsensusreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fgbio=2.2.1 + - bioconda::fgbio=2.4.0 diff --git a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml index 6f3c75600d8..e2c4b144f32 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml +++ b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fgbio=2.2.1 + - bioconda::fgbio=2.4.0 diff --git a/modules/nf-core/fgbio/sortbam/environment.yml b/modules/nf-core/fgbio/sortbam/environment.yml index 6f3c75600d8..e2c4b144f32 100644 --- a/modules/nf-core/fgbio/sortbam/environment.yml +++ b/modules/nf-core/fgbio/sortbam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fgbio=2.2.1 + - bioconda::fgbio=2.4.0 diff --git a/modules/nf-core/fgbio/zipperbams/environment.yml b/modules/nf-core/fgbio/zipperbams/environment.yml index 6f3c75600d8..e2c4b144f32 100644 --- a/modules/nf-core/fgbio/zipperbams/environment.yml +++ b/modules/nf-core/fgbio/zipperbams/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fgbio=2.2.1 + - bioconda::fgbio=2.4.0 From f5897e42410e8cdbba1cf5371510cabfa6956135 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Mon, 11 Nov 2024 12:19:36 -0800 Subject: [PATCH 2/4] chore: update container images --- modules/nf-core/fgbio/callduplexconsensusreads/main.nf | 4 ++-- modules/nf-core/fgbio/callmolecularconsensusreads/main.nf | 4 ++-- modules/nf-core/fgbio/collectduplexseqmetrics/main.nf | 4 ++-- modules/nf-core/fgbio/fastqtobam/main.nf | 4 ++-- modules/nf-core/fgbio/filterconsensusreads/main.nf | 4 ++-- modules/nf-core/fgbio/groupreadsbyumi/main.nf | 4 ++-- modules/nf-core/fgbio/sortbam/main.nf | 4 ++-- modules/nf-core/fgbio/zipperbams/main.nf | 4 ++-- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/main.nf b/modules/nf-core/fgbio/callduplexconsensusreads/main.nf index 30b1f1eb908..0913700431b 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callduplexconsensusreads/main.nf @@ -4,8 +4,8 @@ process FGBIO_CALLDUPLEXCONSENSUSREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' : - 'biocontainers/fgbio:2.2.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' : + 'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }" input: tuple val(meta), path(grouped_bam) diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf index 8a2cdb247e2..7d2e660d02f 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf @@ -4,8 +4,8 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' : - 'biocontainers/fgbio:2.2.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' : + 'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }" input: tuple val(meta), path(grouped_bam) diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf b/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf index d1d6bfc6a14..d86e401acc9 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf @@ -4,8 +4,8 @@ process FGBIO_COLLECTDUPLEXSEQMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-51891ad0b60843e4aade9cde2eb5d40c5ae92b80:72c944cdea5caff7f03b96034968ce2a4f1737bc-0': - 'biocontainers/mulled-v2-51891ad0b60843e4aade9cde2eb5d40c5ae92b80:72c944cdea5caff7f03b96034968ce2a4f1737bc-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d6/d65e7c77d89e7e443384d17a94ffe31fe988b05bc7d695f2a75beaf502721925/data': + 'community.wave.seqera.io/library/fgbio_r-ggplot2:cf2b9a5308d77b67' }" input: tuple val(meta), path(grouped_bam) diff --git a/modules/nf-core/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf index b1c884e863e..b4223db0f8c 100644 --- a/modules/nf-core/fgbio/fastqtobam/main.nf +++ b/modules/nf-core/fgbio/fastqtobam/main.nf @@ -4,8 +4,8 @@ process FGBIO_FASTQTOBAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' : - 'biocontainers/fgbio:2.2.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' : + 'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fgbio/filterconsensusreads/main.nf b/modules/nf-core/fgbio/filterconsensusreads/main.nf index 48379b9c3c0..89d21486d41 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/main.nf +++ b/modules/nf-core/fgbio/filterconsensusreads/main.nf @@ -4,8 +4,8 @@ process FGBIO_FILTERCONSENSUSREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' : - 'biocontainers/fgbio:2.2.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' : + 'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf index da9bf80acee..c0506c90223 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/main.nf +++ b/modules/nf-core/fgbio/groupreadsbyumi/main.nf @@ -4,8 +4,8 @@ process FGBIO_GROUPREADSBYUMI { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' : - 'biocontainers/fgbio:2.2.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' : + 'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/sortbam/main.nf b/modules/nf-core/fgbio/sortbam/main.nf index e061f7caff8..818cdb40a96 100644 --- a/modules/nf-core/fgbio/sortbam/main.nf +++ b/modules/nf-core/fgbio/sortbam/main.nf @@ -4,8 +4,8 @@ process FGBIO_SORTBAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' : - 'biocontainers/fgbio:2.2.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' : + 'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/fgbio/zipperbams/main.nf b/modules/nf-core/fgbio/zipperbams/main.nf index 2316a8ab28b..6ac212138a3 100644 --- a/modules/nf-core/fgbio/zipperbams/main.nf +++ b/modules/nf-core/fgbio/zipperbams/main.nf @@ -4,8 +4,8 @@ process FGBIO_ZIPPERBAMS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fgbio:2.2.1--hdfd78af_0' : - 'biocontainers/fgbio:2.2.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87626ef674e2f19366ae6214575a114fe80ce598e796894820550731706a84be/data' : + 'community.wave.seqera.io/library/fgbio:2.4.0--913bad9d47ff8ddc' }" input: tuple val(meta), path(unmapped_bam) From 6b09e148770bf8ce59c17b7442759df3a82b5265 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Mon, 11 Nov 2024 13:16:25 -0800 Subject: [PATCH 3/4] chore: update snaps --- .../tests/main.nf.test.snap | 20 +++---- .../tests/main.nf.test.snap | 20 +++---- .../tests/main.nf.test.snap | 16 +++--- .../fgbio/fastqtobam/tests/main.nf.test.snap | 56 +++++++++---------- .../tests/main.nf.test.snap | 20 +++---- .../groupreadsbyumi/tests/main.nf.test.snap | 20 +++---- .../fgbio/sortbam/tests/main.nf.test.snap | 20 +++---- .../fgbio/zipperbams/tests/main.nf.test.snap | 24 ++++---- 8 files changed, 98 insertions(+), 98 deletions(-) diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test.snap b/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test.snap index 6966ffabb13..97736281a76 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/callduplexconsensusreads/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7277dba1bc055b578eb6d8d6af43b128" + "versions.yml:md5,b2c92e1b52c4e42b0b1e74ec828feb04" ], "bam": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7277dba1bc055b578eb6d8d6af43b128" + "versions.yml:md5,b2c92e1b52c4e42b0b1e74ec828feb04" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-02T17:44:41.656625835" + "timestamp": "2024-11-11T12:21:15.700422" }, "homo_sapiens - bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7277dba1bc055b578eb6d8d6af43b128" + "versions.yml:md5,b2c92e1b52c4e42b0b1e74ec828feb04" ], "bam": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7277dba1bc055b578eb6d8d6af43b128" + "versions.yml:md5,b2c92e1b52c4e42b0b1e74ec828feb04" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-17T06:05:28.894178772" + "timestamp": "2024-11-11T12:21:02.896452" } } \ No newline at end of file diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test.snap b/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test.snap index 088f99238ca..e7e4507f2d8 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,8a39cbc62685ce7afb5ae36609898bde" + "versions.yml:md5,b5ef59a06877dec12426c4c2c02e887c" ], "bam": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,8a39cbc62685ce7afb5ae36609898bde" + "versions.yml:md5,b5ef59a06877dec12426c4c2c02e887c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-17T06:01:29.676084265" + "timestamp": "2024-11-11T12:22:07.722755" }, "homo_sapiens - bam": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,8a39cbc62685ce7afb5ae36609898bde" + "versions.yml:md5,b5ef59a06877dec12426c4c2c02e887c" ], "bam": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,8a39cbc62685ce7afb5ae36609898bde" + "versions.yml:md5,b5ef59a06877dec12426c4c2c02e887c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:34:16.47828891" + "timestamp": "2024-11-11T12:21:46.241305" } } \ No newline at end of file diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap index 7dfa35f5801..588f8f079c3 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap @@ -41,15 +41,15 @@ ], [ - "versions.yml:md5,637a7384cd910f0e0541a631c52b95e1" + "versions.yml:md5,d19c5782883e16da8a29a27d7074c080" ], "test.duplex_qc.pdf" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T19:26:23.325859809" + "timestamp": "2024-11-11T12:22:45.594572" }, "homo_sapiens - bam": { "content": [ @@ -93,14 +93,14 @@ ], [ - "versions.yml:md5,637a7384cd910f0e0541a631c52b95e1" + "versions.yml:md5,d19c5782883e16da8a29a27d7074c080" ], "test.duplex_qc.pdf" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T19:26:03.1373243" + "timestamp": "2024-11-11T12:22:30.764995" } } \ No newline at end of file diff --git a/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test.snap b/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test.snap index fe9c01cdab8..dd167b97683 100644 --- a/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/fastqtobam/tests/main.nf.test.snap @@ -6,14 +6,14 @@ ], "test.cram", [ - "versions.yml:md5,f6c3db3a20ce5e11c96e0ddd8ccd51de" + "versions.yml:md5,5f78e5611a92d4bd41337180b6d071b3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:35:16.955213727" + "timestamp": "2024-11-11T12:23:19.214068" }, "homo_sapiens - fastq1": { "content": [ @@ -22,14 +22,14 @@ ], [ - "versions.yml:md5,f6c3db3a20ce5e11c96e0ddd8ccd51de" + "versions.yml:md5,5f78e5611a92d4bd41337180b6d071b3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:35:50.320465546" + "timestamp": "2024-11-11T12:23:52.501663" }, "homo_sapiens - [fastq1, fastq2] - default": { "content": [ @@ -38,14 +38,14 @@ ], [ - "versions.yml:md5,f6c3db3a20ce5e11c96e0ddd8ccd51de" + "versions.yml:md5,5f78e5611a92d4bd41337180b6d071b3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:34:53.093519753" + "timestamp": "2024-11-11T12:23:02.561152" }, "homo_sapiens - [fastq1, fastq2] - umi": { "content": [ @@ -54,14 +54,14 @@ ], [ - "versions.yml:md5,f6c3db3a20ce5e11c96e0ddd8ccd51de" + "versions.yml:md5,5f78e5611a92d4bd41337180b6d071b3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:36:07.216840033" + "timestamp": "2024-11-11T12:24:09.020635" }, "homo_sapiens - [fastq1, fastq2] - bam": { "content": [ @@ -70,14 +70,14 @@ ], [ - "versions.yml:md5,f6c3db3a20ce5e11c96e0ddd8ccd51de" + "versions.yml:md5,5f78e5611a92d4bd41337180b6d071b3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:35:33.666898844" + "timestamp": "2024-11-11T12:23:35.97054" }, "homo_sapiens - [fastq1, fastq2] - custom sample": { "content": [ @@ -86,14 +86,14 @@ ], [ - "versions.yml:md5,f6c3db3a20ce5e11c96e0ddd8ccd51de" + "versions.yml:md5,5f78e5611a92d4bd41337180b6d071b3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:36:24.905643178" + "timestamp": "2024-11-11T12:24:25.692023" }, "homo_sapiens - [fastq1, fastq2] - stub": { "content": [ @@ -102,13 +102,13 @@ ], [ - "versions.yml:md5,f6c3db3a20ce5e11c96e0ddd8ccd51de" + "versions.yml:md5,5f78e5611a92d4bd41337180b6d071b3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:36:38.954087571" + "timestamp": "2024-11-11T12:24:37.828713" } } \ No newline at end of file diff --git a/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test.snap b/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test.snap index 5c7f517eda6..5e3b46f0a2d 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/filterconsensusreads/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,63ca8ca45ef2080260cc973288239e7b" + "versions.yml:md5,851cc03732cb4307aa499b822bb80b33" ], "bam": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,63ca8ca45ef2080260cc973288239e7b" + "versions.yml:md5,851cc03732cb4307aa499b822bb80b33" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T06:05:27.436987863" + "timestamp": "2024-11-11T12:25:06.750465" }, "sarscov2 - bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,63ca8ca45ef2080260cc973288239e7b" + "versions.yml:md5,851cc03732cb4307aa499b822bb80b33" ], "bam": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,63ca8ca45ef2080260cc973288239e7b" + "versions.yml:md5,851cc03732cb4307aa499b822bb80b33" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T06:08:24.799849173" + "timestamp": "2024-11-11T12:24:54.71894" } } \ No newline at end of file diff --git a/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test.snap b/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test.snap index dc89a622c76..67956c53370 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/groupreadsbyumi/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,e293eed3614f921114b3bd5b0e1ada10" + "versions.yml:md5,3951d85671eb08c5731449a16bd9a229" ], "bam": [ [ @@ -42,15 +42,15 @@ ] ], "versions": [ - "versions.yml:md5,e293eed3614f921114b3bd5b0e1ada10" + "versions.yml:md5,3951d85671eb08c5731449a16bd9a229" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:48:29.108067677" + "timestamp": "2024-11-11T12:25:36.897639" }, "sarscov2 - bam": { "content": [ @@ -74,7 +74,7 @@ ] ], "2": [ - "versions.yml:md5,e293eed3614f921114b3bd5b0e1ada10" + "versions.yml:md5,3951d85671eb08c5731449a16bd9a229" ], "bam": [ [ @@ -95,14 +95,14 @@ ] ], "versions": [ - "versions.yml:md5,e293eed3614f921114b3bd5b0e1ada10" + "versions.yml:md5,3951d85671eb08c5731449a16bd9a229" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:48:14.269677258" + "timestamp": "2024-11-11T12:25:25.077144" } } \ No newline at end of file diff --git a/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap b/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap index 39761a99d27..6f437ba477d 100644 --- a/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/sortbam/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017" + "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e" ], "bam": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017" + "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T05:37:31.605753331" + "timestamp": "2024-11-11T12:26:05.650691" }, "sarscov2 - bam": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017" + "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e" ], "bam": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,384c5398cae017e4fe0df8cb8f004017" + "versions.yml:md5,2d127286141b26c7cf87e99f2875d10e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:48:47.945706955" + "timestamp": "2024-11-11T12:25:53.613141" } } \ No newline at end of file diff --git a/modules/nf-core/fgbio/zipperbams/tests/main.nf.test.snap b/modules/nf-core/fgbio/zipperbams/tests/main.nf.test.snap index 046c82770e8..ac7f19f7917 100644 --- a/modules/nf-core/fgbio/zipperbams/tests/main.nf.test.snap +++ b/modules/nf-core/fgbio/zipperbams/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,febce3e93c176534d546b12a8766778c" + "versions.yml:md5,14c9cd3297b43902a9a0cb60aea4def4" ], "bam": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,febce3e93c176534d546b12a8766778c" + "versions.yml:md5,14c9cd3297b43902a9a0cb60aea4def4" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:29:48.140540051" + "timestamp": "2024-11-11T12:26:44.653937" }, "sarscov2 - bam": { "content": [ @@ -43,11 +43,11 @@ "id": "test", "single_end": false }, - "test_zipped.bam:md5,b309c59ad774142b42c48b122d1f38bb" + "test_zipped.bam:md5,1980b44177f4720f1005c9be62b09f79" ] ], "1": [ - "versions.yml:md5,febce3e93c176534d546b12a8766778c" + "versions.yml:md5,14c9cd3297b43902a9a0cb60aea4def4" ], "bam": [ [ @@ -55,18 +55,18 @@ "id": "test", "single_end": false }, - "test_zipped.bam:md5,b309c59ad774142b42c48b122d1f38bb" + "test_zipped.bam:md5,1980b44177f4720f1005c9be62b09f79" ] ], "versions": [ - "versions.yml:md5,febce3e93c176534d546b12a8766778c" + "versions.yml:md5,14c9cd3297b43902a9a0cb60aea4def4" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-21T10:31:35.808757537" + "timestamp": "2024-11-11T12:26:29.680188" } } \ No newline at end of file From 69750ddc69174e3693b7c61eba39772c33fa9412 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Tue, 12 Nov 2024 10:49:27 -0800 Subject: [PATCH 4/4] fix: wave build conditional --- .github/workflows/wave.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml index 08e376c50ee..9d33e95648e 100644 --- a/.github/workflows/wave.yml +++ b/.github/workflows/wave.yml @@ -16,7 +16,7 @@ jobs: generate-matrix: name: generate-matrix runs-on: ubuntu-latest - if: github.repository == 'nf-core/modules' + if: github.repository_owner == 'nf-core' steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4