diff --git a/modules.json b/modules.json index 24d7a0a..e43cf69 100644 --- a/modules.json +++ b/modules.json @@ -57,7 +57,7 @@ }, "datavzrd": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "09f36ce2d721684f2883fdde4353c563ea15a48c", "installed_by": ["modules"] }, "happy/happy": { diff --git a/modules/local/create_datavzrd_input/main.nf b/modules/local/create_datavzrd_input/main.nf index 1042dc4..5bf39e3 100644 --- a/modules/local/create_datavzrd_input/main.nf +++ b/modules/local/create_datavzrd_input/main.nf @@ -2,6 +2,11 @@ process CREATE_DATAVZRD_INPUT { tag "$meta.id" label 'process_single' + conda "conda-forge::tar=1.34" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'quay.io/nf-core/ubuntu:20.04' }" + input: tuple val(meta), path(csv), path(template) diff --git a/modules/local/variant_extractor/main.nf b/modules/local/variant_extractor/main.nf index b2bb932..b4ab1e2 100644 --- a/modules/local/variant_extractor/main.nf +++ b/modules/local/variant_extractor/main.nf @@ -4,7 +4,7 @@ process VARIANT_EXTRACTOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/htslib_pysam_tabix_pip_variant-extractor:a12ef217eccf6ba8': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c9964f2ad344f5df543a390ddceb308af0816bed9c9abb9cb400e65525580694/data': 'community.wave.seqera.io/library/htslib_pysam_tabix_pip_variant-extractor:a12ef217eccf6ba8' }" input: diff --git a/modules/local/vcf_to_csv/main.nf b/modules/local/vcf_to_csv/main.nf index f17e7a4..464581a 100644 --- a/modules/local/vcf_to_csv/main.nf +++ b/modules/local/vcf_to_csv/main.nf @@ -4,7 +4,7 @@ process VCF_TO_CSV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/pysam_pandas_pip_variant-extractor:a2d9ec4a4efadbc3': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/30/30151e7153f1f845e2723b29048a3cdf842e2dcb1384cfcc86ced0211d5e4895/data': 'community.wave.seqera.io/library/pysam_pandas_pip_variant-extractor:a2d9ec4a4efadbc3' }" input: diff --git a/modules/nf-core/datavzrd/main.nf b/modules/nf-core/datavzrd/main.nf index a8a6261..c9b6e03 100644 --- a/modules/nf-core/datavzrd/main.nf +++ b/modules/nf-core/datavzrd/main.nf @@ -4,8 +4,8 @@ process DATAVZRD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/datavzrd:2.36.12--bb93c8c988b7a9af': - 'community.wave.seqera.io/library/datavzrd:2.36.12--593eb75e566b7f2a' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c4/c44b3faa30ec68edb0ca92766fb49bd8f526d56c1a034d1acdb0d1448b42adec/data': + 'community.wave.seqera.io/library/datavzrd:2.36.12--dcdc5d4c72e652e2' }" input: tuple val(meta), file(config_file), file(table) diff --git a/tests/.nftignore b/tests/.nftignore index 1b219f2..726ae37 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -19,11 +19,13 @@ references/rtgtools/genome.sdf/done **/summary/datavzrd/**/test/*.{js} **/summary/datavzrd/**/test/index_1.html **/summary/datavzrd/**/test/data/data_1.js -**/summary/datavzrd/**/test/plots/*.{js} -**/summary/datavzrd/**/network/plots/*.{js} +**/summary/datavzrd/**/test/plots/*.js +**/summary/datavzrd/**/network/plots/*.js **/summary/datavzrd/**/network/*.{js} **/summary/datavzrd/**/network/index_1.html **/summary/datavzrd/**/network/data/data_1.js +**/summary/plots/happy/*.png +**/summary/plots/rtgtools/*.png **/summary/plots/**/*.png **/summary/comparisons/*.csv **/summary/tables/**/*.csv diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap index 019291b..a99138b 100644 --- a/tests/germline_small.nf.test.snap +++ b/tests/germline_small.nf.test.snap @@ -229,9 +229,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-22T13:15:43.288411916" + "timestamp": "2024-11-28T16:47:47.024615694" }, "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": { "content": [ @@ -573,8 +573,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-22T13:13:38.90109915" + "timestamp": "2024-11-28T16:45:26.990755841" } } \ No newline at end of file diff --git a/tests/germline_sv.nf.test.snap b/tests/germline_sv.nf.test.snap index ecb99af..b566380 100644 --- a/tests/germline_sv.nf.test.snap +++ b/tests/germline_sv.nf.test.snap @@ -355,9 +355,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-26T14:01:47.145700457" + "timestamp": "2024-11-28T16:51:57.386421371" }, "-stub": { "content": [ @@ -654,8 +654,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-22T12:38:58.811950484" + "timestamp": "2024-11-28T16:54:34.483191183" } } \ No newline at end of file diff --git a/tests/liftover_hg38.nf.test.snap b/tests/liftover_hg38.nf.test.snap index fc7dce1..55af699 100644 --- a/tests/liftover_hg38.nf.test.snap +++ b/tests/liftover_hg38.nf.test.snap @@ -349,9 +349,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-22T13:34:14.298465035" + "timestamp": "2024-11-29T09:23:31.648065377" }, "-stub": { "content": [ diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap index 81eb1c4..fabf609 100644 --- a/tests/somatic_sv.nf.test.snap +++ b/tests/somatic_sv.nf.test.snap @@ -204,8 +204,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-26T13:55:27.662287528" + "timestamp": "2024-11-28T16:58:12.671419675" } } \ No newline at end of file