From b07efecf2b2666f28480a723241394a89ccb43c1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 21 Oct 2024 16:30:07 +0200 Subject: [PATCH 1/4] vep_update --- modules.json | 4 ++-- modules/nf-core/ensemblvep/filtervep/environment.yml | 2 +- modules/nf-core/ensemblvep/filtervep/main.nf | 4 ++-- .../nf-core/ensemblvep/filtervep/tests/main.nf.test | 6 +++--- .../ensemblvep/filtervep/tests/main.nf.test.snap | 12 ++++++------ .../ensemblvep/filtervep/tests/nextflow.config | 10 +++++----- .../nf-core/ensemblvep/filtervep/tests/tab.gz.config | 8 ++++---- .../nf-core/ensemblvep/filtervep/tests/vcf.config | 6 +++--- modules/nf-core/ensemblvep/vep/environment.yml | 2 +- modules/nf-core/ensemblvep/vep/main.nf | 4 ++-- modules/nf-core/ensemblvep/vep/tests/main.nf.test | 6 +++--- .../nf-core/ensemblvep/vep/tests/main.nf.test.snap | 12 ++++++------ modules/nf-core/ensemblvep/vep/tests/nextflow.config | 2 +- 13 files changed, 39 insertions(+), 39 deletions(-) diff --git a/modules.json b/modules.json index c60414da..6f4dce4e 100644 --- a/modules.json +++ b/modules.json @@ -123,12 +123,12 @@ }, "ensemblvep/filtervep": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", "installed_by": ["modules"] }, "expansionhunter": { diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index 283a45bb..3d36eb17 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ensembl-vep=112.0 + - bioconda::ensembl-vep=113.0 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index a56bdb83..69245df0 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_FILTERVEP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test index 1852e2ab..7147792f 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test @@ -23,7 +23,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"112_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version @@ -84,7 +84,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"112_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version @@ -129,7 +129,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out.versions).match() }, - { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v112.0") } + { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") } ) } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index ddaa1dc1..065d747b 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -2,25 +2,25 @@ "test_ensemblvep_filtervep_vcf": { "content": [ [ - "versions.yml:md5,4d3217834548bbe6784e102e9348461d" + "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:38:25.18143" + "timestamp": "2024-10-21T09:10:47.874831491" }, "test_ensemblvep_filtervep_tab_gz": { "content": [ [ - "versions.yml:md5,4d3217834548bbe6784e102e9348461d" + "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:57:11.471669" + "timestamp": "2024-10-21T09:11:18.765461163" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config index aee2e62b..40b3a3bd 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config @@ -1,10 +1,10 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ params { - vep_cache_version = "112" - vep_genome = "WBcel235" - vep_species = "caenorhabditis_elegans" + vep_cache_version = "113" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config index 0aa5ea75..cdad2d94 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ process { @@ -13,12 +13,12 @@ process { } withName: ENSEMBLVEP_VEP { - ext.args = '--tab' + ext.args = '--tab' ext.prefix = { "${meta.id}_vep" } } withName: ENSEMBLVEP_FILTERVEP { - ext.args = '--filter "Feature_type is Transcript"' + ext.args = '--filter "Feature_type is Transcript"' ext.suffix = "tab" } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config index 0b65fe5c..ee2aef57 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ process { @@ -13,7 +13,7 @@ process { } withName: ENSEMBLVEP_VEP { - ext.args = '--vcf' + ext.args = '--vcf' ext.prefix = { "${meta.id}_vep" } } diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 283a45bb..3d36eb17 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ensembl-vep=112.0 + - bioconda::ensembl-vep=113.0 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 5f33265b..7d2c82ff 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(vcf), path(custom_extra_files) diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test index e68fff3c..3e8c0b53 100644 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -21,7 +21,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"112_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version @@ -72,7 +72,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"112_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version @@ -107,7 +107,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out.versions).match() }, - { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v112.0") } + { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") } ) } } diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap index 1c4c0e4e..1df94276 100644 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -2,25 +2,25 @@ "test_ensemblvep_vep_fasta_tab_gz": { "content": [ [ - "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559" + "versions.yml:md5,4fbfeb73f0d4b4aa039f17be8ba9e1f2" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T10:15:18.228927" + "timestamp": "2024-10-21T09:12:23.474703494" }, "test_ensemblvep_vep_fasta_vcf": { "content": [ [ - "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559" + "versions.yml:md5,4fbfeb73f0d4b4aa039f17be8ba9e1f2" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T10:14:50.193861" + "timestamp": "2024-10-21T09:11:54.343590485" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config index 9aa48164..0a4ae1a6 100644 --- a/modules/nf-core/ensemblvep/vep/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -1,5 +1,5 @@ params { - vep_cache_version = "112" + vep_cache_version = "113" vep_genome = "WBcel235" vep_species = "caenorhabditis_elegans" } From 4e7df988bbda3de7097f37c414db297086d8cbf5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 21 Oct 2024 16:30:44 +0200 Subject: [PATCH 2/4] update changelog --- CHANGELOG.md | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 038b7090..25fae31a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,17 +28,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| -------- | ----------- | ----------- | -| bcftools | 1.18 | 1.20 | -| genmod | 3.8.2 | 3.8.3 | -| mosdepth | 0.3.6 | 0.3.8 | -| multiqc | 1.21 | 1.25.1 | -| picard | 3.1.1 | 3.2.0 | -| samtools | 1.19.2 | 1.21 | -| sentieon | 202308.02 | 202308.03 | -| stranger | 0.8.1 | 0.9.1 | -| tabix | 1.19.1 | 1.20 | +| Tool | Old version | New version | +| ---------- | ----------- | ----------- | +| bcftools | 1.18 | 1.20 | +| ensemblvep | 112 | 113 | +| genmod | 3.8.2 | 3.8.3 | +| mosdepth | 0.3.6 | 0.3.8 | +| multiqc | 1.21 | 1.25.1 | +| picard | 3.1.1 | 3.2.0 | +| samtools | 1.19.2 | 1.21 | +| sentieon | 202308.02 | 202308.03 | +| stranger | 0.8.1 | 0.9.1 | +| tabix | 1.19.1 | 1.20 | ## 2.2.0 - Dogmatix [2024-09-13] From b3ff4703ff7d2e4b872d501429cd588a1b861691 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 22 Oct 2024 13:13:26 +0200 Subject: [PATCH 3/4] update conf --- conf/modules/annotate_mobile_elements.config | 2 +- conf/modules/annotate_mt_snvs.config | 2 +- conf/modules/annotate_structural_variants.config | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/modules/annotate_mobile_elements.config b/conf/modules/annotate_mobile_elements.config index 7d001727..b7ffd45a 100644 --- a/conf/modules/annotate_mobile_elements.config +++ b/conf/modules/annotate_mobile_elements.config @@ -37,7 +37,7 @@ process { '--appris --biotype --buffer_size 100 --canonical --cache --ccds', '--compress_output bgzip --distance 5000 --domains', '--exclude_predicted --force_overwrite --format vcf', - '--fork 4 --hgvs --humdiv --max_sv_size 248956422 --merged', + '--hgvs --humdiv --max_sv_size 248956422 --merged', '--no_progress --numbers --per_gene --polyphen p', '--protein --offline --regulatory --sift p', '--symbol --tsl --uniprot --vcf' diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config index 0d0026cf..c8b1de52 100644 --- a/conf/modules/annotate_mt_snvs.config +++ b/conf/modules/annotate_mt_snvs.config @@ -29,7 +29,7 @@ process { '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz', '--distance 0', '--buffer_size 20000', - '--format vcf --fork 4 --max_sv_size 248956422', + '--format vcf --max_sv_size 248956422', '--appris --biotype --cache --canonical --ccds --compress_output bgzip', '--domains --exclude_predicted --force_overwrite', '--hgvs --humdiv --no_progress --numbers', diff --git a/conf/modules/annotate_structural_variants.config b/conf/modules/annotate_structural_variants.config index 07725c24..75216efd 100644 --- a/conf/modules/annotate_structural_variants.config +++ b/conf/modules/annotate_structural_variants.config @@ -37,14 +37,14 @@ process { withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV' { ext.args = { [ - '--dir_cache vep_cache', - '--dir_plugins vep_cache/Plugins', + '--dir_cache cache', + '--dir_plugins cache/Plugins', '--plugin pLI,pLI_values.txt', '--appris --biotype --buffer_size 100 --canonical --cache --ccds', '--compress_output bgzip --distance 5000 --domains', '--exclude_predicted --force_overwrite --format vcf', - '--fork 4 --hgvs --humdiv --max_sv_size 248956422 --merged', - '--no_progress --numbers --per_gene --polyphen p', + '--hgvs --humdiv --max_sv_size 248956422 --merged', + '--dont_skip --no_progress --numbers --per_gene --polyphen p', '--protein --offline --regulatory --sift p', '--symbol --tsl --uniprot --vcf' ].join(' ') } From 07dfe9ab00c25d5f7a4bb5f9cf9cd82dd5de4f1d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 22 Oct 2024 14:07:34 +0200 Subject: [PATCH 4/4] update config --- conf/modules/annotate_structural_variants.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/annotate_structural_variants.config b/conf/modules/annotate_structural_variants.config index 75216efd..b8af1e88 100644 --- a/conf/modules/annotate_structural_variants.config +++ b/conf/modules/annotate_structural_variants.config @@ -44,7 +44,7 @@ process { '--compress_output bgzip --distance 5000 --domains', '--exclude_predicted --force_overwrite --format vcf', '--hgvs --humdiv --max_sv_size 248956422 --merged', - '--dont_skip --no_progress --numbers --per_gene --polyphen p', + '--no_progress --numbers --per_gene --polyphen p', '--protein --offline --regulatory --sift p', '--symbol --tsl --uniprot --vcf' ].join(' ') }