From faf5a37f361d995ccafc0521c7fd2d51218b0a29 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Wed, 22 Jan 2025 10:31:48 +0900 Subject: [PATCH] Update to LAST version 1608 using sequera containers. This version will be needed for the use of the new maf-linked tool later. --- modules/nf-core/last/dotplot/environment.yml | 2 +- modules/nf-core/last/dotplot/main.nf | 6 ++-- .../last/dotplot/tests/main.nf.test.snap | 12 ++++---- modules/nf-core/last/lastal/environment.yml | 2 +- modules/nf-core/last/lastal/main.nf | 6 ++-- .../last/lastal/tests/main.nf.test.snap | 30 +++++++++---------- modules/nf-core/last/lastdb/environment.yml | 2 +- modules/nf-core/last/lastdb/main.nf | 6 ++-- .../last/lastdb/tests/main.nf.test.snap | 26 ++++++++-------- .../nf-core/last/mafconvert/environment.yml | 2 +- modules/nf-core/last/mafconvert/main.nf | 6 ++-- .../last/mafconvert/tests/main.nf.test.snap | 12 ++++---- modules/nf-core/last/mafswap/environment.yml | 2 +- modules/nf-core/last/mafswap/main.nf | 6 ++-- .../nf-core/last/mafswap/tests/main.nf.test | 2 +- .../last/mafswap/tests/main.nf.test.snap | 12 ++++---- modules/nf-core/last/postmask/environment.yml | 2 +- modules/nf-core/last/postmask/main.nf | 6 ++-- .../last/postmask/tests/main.nf.test.snap | 12 ++++---- modules/nf-core/last/split/environment.yml | 2 +- modules/nf-core/last/split/main.nf | 6 ++-- .../last/split/tests/main.nf.test.snap | 12 ++++---- modules/nf-core/last/train/environment.yml | 2 +- modules/nf-core/last/train/main.nf | 6 ++-- .../last/train/tests/main.nf.test.snap | 20 ++++++------- 25 files changed, 101 insertions(+), 101 deletions(-) diff --git a/modules/nf-core/last/dotplot/environment.yml b/modules/nf-core/last/dotplot/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/dotplot/environment.yml +++ b/modules/nf-core/last/dotplot/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index da11ceba322..963965bd1c3 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -3,9 +3,9 @@ process LAST_DOTPLOT { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(maf), path(annot_b) diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test.snap b/modules/nf-core/last/dotplot/tests/main.nf.test.snap index f27ae3e6b19..3676f0f4c20 100644 --- a/modules/nf-core/last/dotplot/tests/main.nf.test.snap +++ b/modules/nf-core/last/dotplot/tests/main.nf.test.snap @@ -2,37 +2,37 @@ "sarscov2 - contigs - genome - gif": { "content": [ [ - "versions.yml:md5,4faa6f4aecf50e689d84709648818a9f" + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:22:21.508978" + "timestamp": "2025-01-21T09:18:32.629314" }, "sarscov2 - contigs - genome - png - stub": { "content": [ [ - "versions.yml:md5,4faa6f4aecf50e689d84709648818a9f" + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:22:37.504391" + "timestamp": "2025-01-21T09:18:48.084683" }, "sarscov2 - contigs - genome - png": { "content": [ [ - "versions.yml:md5,4faa6f4aecf50e689d84709648818a9f" + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:22:05.800777" + "timestamp": "2025-01-21T09:18:17.971205" } } \ No newline at end of file diff --git a/modules/nf-core/last/lastal/environment.yml b/modules/nf-core/last/lastal/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/lastal/environment.yml +++ b/modules/nf-core/last/lastal/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf index 73369a86928..9cd11d4b6ca 100644 --- a/modules/nf-core/last/lastal/main.nf +++ b/modules/nf-core/last/lastal/main.nf @@ -3,9 +3,9 @@ process LAST_LASTAL { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(fastx), path (param_file) diff --git a/modules/nf-core/last/lastal/tests/main.nf.test.snap b/modules/nf-core/last/lastal/tests/main.nf.test.snap index 23705f7d04c..50cc114a48d 100644 --- a/modules/nf-core/last/lastal/tests/main.nf.test.snap +++ b/modules/nf-core/last/lastal/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,fac3fd9e98f2fac019e09d434634e542" + "contigs.maf.gz:md5,3729bf099fecb196b8b5b49fc3487b56" ] ], "1": [ @@ -17,11 +17,11 @@ "id": "contigs", "single_end": false }, - "contigs.tsv:md5,f028e69bd64e54080b9a03fd809cba74" + "contigs.tsv:md5,38d678f139ea70765ce29966c743487b" ] ], "2": [ - "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5" + "versions.yml:md5,23bb5d428e31caed85e991482fa9f967" ], "maf": [ [ @@ -29,7 +29,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,fac3fd9e98f2fac019e09d434634e542" + "contigs.maf.gz:md5,3729bf099fecb196b8b5b49fc3487b56" ] ], "multiqc": [ @@ -38,11 +38,11 @@ "id": "contigs", "single_end": false }, - "contigs.tsv:md5,f028e69bd64e54080b9a03fd809cba74" + "contigs.tsv:md5,38d678f139ea70765ce29966c743487b" ] ], "versions": [ - "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5" + "versions.yml:md5,23bb5d428e31caed85e991482fa9f967" ] } ], @@ -50,7 +50,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:27:20.528278" + "timestamp": "2025-01-22T10:13:12.144354" }, "sarscov2 - contigs - genome - stub": { "content": [ @@ -74,7 +74,7 @@ ] ], "2": [ - "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5" + "versions.yml:md5,23bb5d428e31caed85e991482fa9f967" ], "maf": [ [ @@ -95,7 +95,7 @@ ] ], "versions": [ - "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5" + "versions.yml:md5,23bb5d428e31caed85e991482fa9f967" ] } ], @@ -103,7 +103,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:28:03.933791" + "timestamp": "2025-01-22T10:15:14.385573" }, "sarscov2 - contigs - genome - withparams": { "content": [ @@ -114,7 +114,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,5c4e2c43ed5371453a88a72586577f39" + "contigs.maf.gz:md5,b2ea256c960899555dbc3fd1acbc43b4" ] ], "1": [ @@ -127,7 +127,7 @@ ] ], "2": [ - "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5" + "versions.yml:md5,23bb5d428e31caed85e991482fa9f967" ], "maf": [ [ @@ -135,7 +135,7 @@ "id": "contigs", "single_end": false }, - "contigs.maf.gz:md5,5c4e2c43ed5371453a88a72586577f39" + "contigs.maf.gz:md5,b2ea256c960899555dbc3fd1acbc43b4" ] ], "multiqc": [ @@ -148,7 +148,7 @@ ] ], "versions": [ - "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5" + "versions.yml:md5,23bb5d428e31caed85e991482fa9f967" ] } ], @@ -156,6 +156,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:27:42.180309" + "timestamp": "2025-01-22T10:14:13.280646" } } \ No newline at end of file diff --git a/modules/nf-core/last/lastdb/environment.yml b/modules/nf-core/last/lastdb/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/lastdb/environment.yml +++ b/modules/nf-core/last/lastdb/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 1476dd487cc..c69eeb6e325 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -3,9 +3,9 @@ process LAST_LASTDB { label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test.snap b/modules/nf-core/last/lastdb/tests/main.nf.test.snap index 5ccd1923b84..41f3116ef95 100644 --- a/modules/nf-core/last/lastdb/tests/main.nf.test.snap +++ b/modules/nf-core/last/lastdb/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "1": [ - "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1" + "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e" ], "index": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1" + "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:28:57.035523" + "timestamp": "2025-01-22T10:16:49.233187" }, "sarscov2 - fastq gzipped": { "content": [ @@ -59,7 +59,7 @@ [ "test.bck:md5,05b14d8ac418b3193d9cc921086cea05", "test.des:md5,26ab49015cc572172b9efa50fc5190bc", - "test.prj:md5,94d4c9b51136494870775837d7e7f06c", + "test.prj:md5,a9e1fa5d50afd39e57aaab489ca2b0a2", "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b", "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da", "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0", @@ -68,7 +68,7 @@ ] ], "1": [ - "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1" + "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e" ], "index": [ [ @@ -78,7 +78,7 @@ [ "test.bck:md5,05b14d8ac418b3193d9cc921086cea05", "test.des:md5,26ab49015cc572172b9efa50fc5190bc", - "test.prj:md5,94d4c9b51136494870775837d7e7f06c", + "test.prj:md5,a9e1fa5d50afd39e57aaab489ca2b0a2", "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b", "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da", "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0", @@ -87,7 +87,7 @@ ] ], "versions": [ - "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1" + "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e" ] } ], @@ -95,7 +95,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:28:40.861818" + "timestamp": "2025-01-22T10:16:13.506203" }, "sarscov2 - fasta": { "content": [ @@ -108,7 +108,7 @@ [ "test.bck:md5,157526d333b88523cb15ac4efe00738f", "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc", - "test.prj:md5,73136d767ab23467bd6fd80b85376369", + "test.prj:md5,10b52b9f5adad3b9afd3d73897e588f9", "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015", "test.ssp:md5,53524efdea3d8989201419a29e81ec1f", "test.suf:md5,ef7482260705bb8146acbbbdce6c0068", @@ -117,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1" + "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e" ], "index": [ [ @@ -127,7 +127,7 @@ [ "test.bck:md5,157526d333b88523cb15ac4efe00738f", "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc", - "test.prj:md5,73136d767ab23467bd6fd80b85376369", + "test.prj:md5,10b52b9f5adad3b9afd3d73897e588f9", "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015", "test.ssp:md5,53524efdea3d8989201419a29e81ec1f", "test.suf:md5,ef7482260705bb8146acbbbdce6c0068", @@ -136,7 +136,7 @@ ] ], "versions": [ - "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1" + "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e" ] } ], @@ -144,6 +144,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:28:25.358778" + "timestamp": "2025-01-22T10:15:48.482722" } } \ No newline at end of file diff --git a/modules/nf-core/last/mafconvert/environment.yml b/modules/nf-core/last/mafconvert/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/mafconvert/environment.yml +++ b/modules/nf-core/last/mafconvert/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 4c88c36fe31..3f02ed7bfeb 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -3,9 +3,9 @@ process LAST_MAFCONVERT { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap index 98c908fc28c..8525a41cc4a 100644 --- a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap +++ b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap @@ -35,7 +35,7 @@ ], "9": [ - "versions.yml:md5,e831f54a26b0f70d8339969112cf0ad5" + "versions.yml:md5,7c66667735aa9f79367b8b8fc8df4497" ], "axt_gz": [ @@ -70,7 +70,7 @@ ], "versions": [ - "versions.yml:md5,e831f54a26b0f70d8339969112cf0ad5" + "versions.yml:md5,7c66667735aa9f79367b8b8fc8df4497" ] } ], @@ -78,7 +78,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:29:34.869839" + "timestamp": "2025-01-22T10:17:48.535961" }, "sarscov2 - bam": { "content": [ @@ -116,7 +116,7 @@ ], "9": [ - "versions.yml:md5,e831f54a26b0f70d8339969112cf0ad5" + "versions.yml:md5,7c66667735aa9f79367b8b8fc8df4497" ], "axt_gz": [ @@ -151,7 +151,7 @@ ], "versions": [ - "versions.yml:md5,e831f54a26b0f70d8339969112cf0ad5" + "versions.yml:md5,7c66667735aa9f79367b8b8fc8df4497" ] } ], @@ -159,6 +159,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:29:19.004671" + "timestamp": "2025-01-22T10:17:13.689118" } } \ No newline at end of file diff --git a/modules/nf-core/last/mafswap/environment.yml b/modules/nf-core/last/mafswap/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/mafswap/environment.yml +++ b/modules/nf-core/last/mafswap/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 39d041d4d05..811e4a9807c 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -3,9 +3,9 @@ process LAST_MAFSWAP { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/mafswap/tests/main.nf.test b/modules/nf-core/last/mafswap/tests/main.nf.test index ae4d7f0ae65..deacc7cc374 100644 --- a/modules/nf-core/last/mafswap/tests/main.nf.test +++ b/modules/nf-core/last/mafswap/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'contigs.genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] """ } diff --git a/modules/nf-core/last/mafswap/tests/main.nf.test.snap b/modules/nf-core/last/mafswap/tests/main.nf.test.snap index 7a6a2231ee7..8c5b39ab0c1 100644 --- a/modules/nf-core/last/mafswap/tests/main.nf.test.snap +++ b/modules/nf-core/last/mafswap/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,85000544798e9ca3417a3f77a57c50b1" + "versions.yml:md5,71e18c05330e522695f775a9fb1375af" ], "maf": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,85000544798e9ca3417a3f77a57c50b1" + "versions.yml:md5,71e18c05330e522695f775a9fb1375af" ] } ], @@ -30,7 +30,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:29:54.600472" + "timestamp": "2025-01-22T10:19:10.413649" }, "sarscov2 - contigs - genome - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,85000544798e9ca3417a3f77a57c50b1" + "versions.yml:md5,71e18c05330e522695f775a9fb1375af" ], "maf": [ [ @@ -55,7 +55,7 @@ ] ], "versions": [ - "versions.yml:md5,85000544798e9ca3417a3f77a57c50b1" + "versions.yml:md5,71e18c05330e522695f775a9fb1375af" ] } ], @@ -63,6 +63,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:30:12.49493" + "timestamp": "2025-01-22T10:19:50.695101" } } \ No newline at end of file diff --git a/modules/nf-core/last/postmask/environment.yml b/modules/nf-core/last/postmask/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/postmask/environment.yml +++ b/modules/nf-core/last/postmask/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index e30787cf5ef..c4d0510d524 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -3,9 +3,9 @@ process LAST_POSTMASK { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/postmask/tests/main.nf.test.snap b/modules/nf-core/last/postmask/tests/main.nf.test.snap index 24d0dde61cd..46ae8dd269f 100644 --- a/modules/nf-core/last/postmask/tests/main.nf.test.snap +++ b/modules/nf-core/last/postmask/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,04d0682aabbbcd7619e50de0cb049e62" + "versions.yml:md5,742f38ac50746578d28d241baff0da7e" ], "maf": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,04d0682aabbbcd7619e50de0cb049e62" + "versions.yml:md5,742f38ac50746578d28d241baff0da7e" ] } ], @@ -30,7 +30,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:30:33.686959" + "timestamp": "2025-01-22T10:20:14.504052" }, "sarscov2 - contigs - genome - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,04d0682aabbbcd7619e50de0cb049e62" + "versions.yml:md5,742f38ac50746578d28d241baff0da7e" ], "maf": [ [ @@ -55,7 +55,7 @@ ] ], "versions": [ - "versions.yml:md5,04d0682aabbbcd7619e50de0cb049e62" + "versions.yml:md5,742f38ac50746578d28d241baff0da7e" ] } ], @@ -63,6 +63,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:30:50.067406" + "timestamp": "2025-01-22T10:20:49.89524" } } \ No newline at end of file diff --git a/modules/nf-core/last/split/environment.yml b/modules/nf-core/last/split/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/split/environment.yml +++ b/modules/nf-core/last/split/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index bead72b52dd..b45879b0dbc 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -3,9 +3,9 @@ process LAST_SPLIT { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(maf) diff --git a/modules/nf-core/last/split/tests/main.nf.test.snap b/modules/nf-core/last/split/tests/main.nf.test.snap index ffaaf19a739..9a65380e37b 100644 --- a/modules/nf-core/last/split/tests/main.nf.test.snap +++ b/modules/nf-core/last/split/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,03867913088efc724e378b633a0d75d6" + "versions.yml:md5,a6fba12ee7bdf891a38befef38775071" ], "maf": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,03867913088efc724e378b633a0d75d6" + "versions.yml:md5,a6fba12ee7bdf891a38befef38775071" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:31:12.936288" + "timestamp": "2025-01-22T10:21:13.045466" }, "sarscov2 - contigs_genome - stub": { "content": [ @@ -68,7 +68,7 @@ ] ], "2": [ - "versions.yml:md5,03867913088efc724e378b633a0d75d6" + "versions.yml:md5,a6fba12ee7bdf891a38befef38775071" ], "maf": [ [ @@ -87,7 +87,7 @@ ] ], "versions": [ - "versions.yml:md5,03867913088efc724e378b633a0d75d6" + "versions.yml:md5,a6fba12ee7bdf891a38befef38775071" ] } ], @@ -95,6 +95,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T18:31:30.192165" + "timestamp": "2025-01-22T10:21:48.04855" } } \ No newline at end of file diff --git a/modules/nf-core/last/train/environment.yml b/modules/nf-core/last/train/environment.yml index 28989363674..7db722d9b7c 100644 --- a/modules/nf-core/last/train/environment.yml +++ b/modules/nf-core/last/train/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda dependencies: - - bioconda::last=1595 + - bioconda::last=1608 diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 3d723f0c5e9..259415a5578 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -3,9 +3,9 @@ process LAST_TRAIN { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' : - 'biocontainers/last:1595--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' + : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" input: tuple val(meta), path(fastx) diff --git a/modules/nf-core/last/train/tests/main.nf.test.snap b/modules/nf-core/last/train/tests/main.nf.test.snap index 4953eb75dbe..db0a002dcfa 100644 --- a/modules/nf-core/last/train/tests/main.nf.test.snap +++ b/modules/nf-core/last/train/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,9e503cefcda96d89f165ec5baee771e2" + "versions.yml:md5,b2d4a4fce93a910c90768053127969b3" ], "multiqc": [ [ @@ -42,7 +42,7 @@ ] ], "versions": [ - "versions.yml:md5,9e503cefcda96d89f165ec5baee771e2" + "versions.yml:md5,b2d4a4fce93a910c90768053127969b3" ] } ], @@ -50,7 +50,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-18T16:45:33.294693" + "timestamp": "2025-01-22T10:23:11.655537" }, "sarscov2 - genome - contigs": { "content": [ @@ -61,7 +61,7 @@ "id": "contigs", "single_end": false }, - "contigs.train:md5,08224a0abf1197d5c2c5b783ffd7bc0c" + "contigs.train:md5,4b965e8de2fa644a196547cb487abc4e" ] ], "1": [ @@ -70,11 +70,11 @@ "id": "contigs", "single_end": false }, - "contigs.train.tsv:md5,f52ce6c55d5f9cde24ab4f9c3b2c27ff" + "contigs.train.tsv:md5,a2fca4aabda82f0aa481085ce5258886" ] ], "2": [ - "versions.yml:md5,69e12df6fa92e2329c90ed3df87aa068" + "versions.yml:md5,c1f06f4162a8b4ee1b8094d967f6678d" ], "multiqc": [ [ @@ -82,7 +82,7 @@ "id": "contigs", "single_end": false }, - "contigs.train.tsv:md5,f52ce6c55d5f9cde24ab4f9c3b2c27ff" + "contigs.train.tsv:md5,a2fca4aabda82f0aa481085ce5258886" ] ], "param_file": [ @@ -91,11 +91,11 @@ "id": "contigs", "single_end": false }, - "contigs.train:md5,08224a0abf1197d5c2c5b783ffd7bc0c" + "contigs.train:md5,4b965e8de2fa644a196547cb487abc4e" ] ], "versions": [ - "versions.yml:md5,69e12df6fa92e2329c90ed3df87aa068" + "versions.yml:md5,c1f06f4162a8b4ee1b8094d967f6678d" ] } ], @@ -103,6 +103,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2024-12-18T16:45:09.643714" + "timestamp": "2025-01-22T10:22:21.360808" } } \ No newline at end of file