From cd571e6bdd1ddf3ad40e9df3f8181d4178ec72a4 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 22 Jul 2024 14:45:16 +1200 Subject: [PATCH] Updated SYRI to 1.7.0 --- CHANGELOG.md | 11 +++++----- modules.json | 16 +++++++++----- modules/{pfr => gallvp}/syri/environment.yml | 2 +- modules/{pfr => gallvp}/syri/main.nf | 4 ++-- modules/{pfr => gallvp}/syri/meta.yml | 0 .../{pfr => gallvp}/syri/tests/main.nf.test | 21 ++++++++++--------- .../syri/tests/main.nf.test.snap | 16 +++++++------- .../syri/tests/nextflow.config | 0 modules/pfr/syri/tests/tags.yml | 2 -- subworkflows/local/fasta_synteny.nf | 2 +- 10 files changed, 40 insertions(+), 34 deletions(-) rename modules/{pfr => gallvp}/syri/environment.yml (88%) rename modules/{pfr => gallvp}/syri/main.nf (92%) rename modules/{pfr => gallvp}/syri/meta.yml (100%) rename modules/{pfr => gallvp}/syri/tests/main.nf.test (56%) rename modules/{pfr => gallvp}/syri/tests/main.nf.test.snap (79%) rename modules/{pfr => gallvp}/syri/tests/nextflow.config (100%) delete mode 100644 modules/pfr/syri/tests/tags.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 320a7a78..e4c4b446 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,16 +13,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 4. Added a test to verify the fix for the bug which resulted in a pipeline crash for assemblies without LTRs 5. Locally patched `FASTA_LTRRETRIEVER_LAI` sub-workflow to emit the `LTRRETRIEVER_LTRRETRIEVER` log as one of the outputs 6. Locally patched `LTRRETRIEVER_LTRRETRIEVER` module to not fail when `LTR_retriever` exits with an error +7. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93) +8. Updated `SYRI` to 1.7.0 [#104](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/104) ### `Fixed` 1. Fixed a bug where `intron_length_distribution` was used instead of `cds_length_distribution` when creating the CDS Length Distribution Graph [#95](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/95) 2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false -3. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93) -4. Now NCBI FCS GX module uses all the cores available from the Nextflow task -5. Fixed a bug which caused `PLOTSR` to fail for certain assembly names [#102](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/102) -6. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly does not contain any LTRs [#92](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/92) -7. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly is not writable [#98](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/98) +3. Now NCBI FCS GX module uses all the cores available from the Nextflow task +4. Fixed a bug which caused `PLOTSR` to fail for certain assembly names [#102](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/102) +5. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly does not contain any LTRs [#92](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/92) +6. Now `LTRRETRIEVER_LTRRETRIEVER` does not crash when the input assembly is not writable [#98](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/98) ### `Dependencies` diff --git a/modules.json b/modules.json index e06755fd..b6151a0c 100644 --- a/modules.json +++ b/modules.json @@ -2,6 +2,17 @@ "name": "plant-food-research-open/assemblyqc", "homePage": "https://github.com/plant-food-research-open/assemblyqc", "repos": { + "https://github.com/GallVp/nxf-components.git": { + "modules": { + "gallvp": { + "syri": { + "branch": "main", + "git_sha": "836bb223521eeaa08d65c1b7f4b82be1272a1964", + "installed_by": ["modules"] + } + } + } + }, "https://github.com/PlantandFoodResearch/nxf-modules.git": { "modules": { "pfr": { @@ -104,11 +115,6 @@ "branch": "main", "git_sha": "84f31d4be03e2ae6bee8e0b9fdea466be8e997bb", "installed_by": ["gff3_gt_gff3_gff3validator_stat"] - }, - "syri": { - "branch": "main", - "git_sha": "295e1d8666c746cb05e79563393035e81c9739fc", - "installed_by": ["modules"] } } }, diff --git a/modules/pfr/syri/environment.yml b/modules/gallvp/syri/environment.yml similarity index 88% rename from modules/pfr/syri/environment.yml rename to modules/gallvp/syri/environment.yml index 45eafb1f..0a34f206 100644 --- a/modules/pfr/syri/environment.yml +++ b/modules/gallvp/syri/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::syri=1.6.3" + - "bioconda::syri=1.7.0" diff --git a/modules/pfr/syri/main.nf b/modules/gallvp/syri/main.nf similarity index 92% rename from modules/pfr/syri/main.nf rename to modules/gallvp/syri/main.nf index 0a10ae19..655018b5 100644 --- a/modules/pfr/syri/main.nf +++ b/modules/gallvp/syri/main.nf @@ -4,8 +4,8 @@ process SYRI { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/syri:1.6.3--py38hdbdd923_2': - 'biocontainers/syri:1.6.3--py38hdbdd923_2' }" + 'https://depot.galaxyproject.org/singularity/syri:1.7.0--py310hdbdd923_0': + 'biocontainers/syri:1.7.0--py310hdbdd923_0' }" input: tuple val(meta), path(infile) diff --git a/modules/pfr/syri/meta.yml b/modules/gallvp/syri/meta.yml similarity index 100% rename from modules/pfr/syri/meta.yml rename to modules/gallvp/syri/meta.yml diff --git a/modules/pfr/syri/tests/main.nf.test b/modules/gallvp/syri/tests/main.nf.test similarity index 56% rename from modules/pfr/syri/tests/main.nf.test rename to modules/gallvp/syri/tests/main.nf.test index baa8555c..27f4f8b3 100644 --- a/modules/pfr/syri/tests/main.nf.test +++ b/modules/gallvp/syri/tests/main.nf.test @@ -6,26 +6,27 @@ nextflow_process { process "SYRI" tag "modules" - tag "modules_nfcore" + tag "modules_gallvp" tag "syri" tag "minimap2/align" setup { run("MINIMAP2_ALIGN") { - script "modules/pfr/minimap2/align/main.nf" + script "../../minimap2/align" process { """ input[0] = [ [id: 'test'], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[1] = [ [id: 'reference'], - file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) ] input[2] = true // bam_format - input[3] = false // cigar_paf_format - input[4] = false // cigar_bam + input[3] = 'bai' // bam_index_extension + input[4] = false // cigar_paf_format + input[5] = false // cigar_bam """ } } @@ -37,8 +38,8 @@ nextflow_process { process { """ input[0] = MINIMAP2_ALIGN.out.bam - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) input[3] = 'B' """ } @@ -61,8 +62,8 @@ nextflow_process { process { """ input[0] = MINIMAP2_ALIGN.out.bam - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) input[3] = 'B' """ } diff --git a/modules/pfr/syri/tests/main.nf.test.snap b/modules/gallvp/syri/tests/main.nf.test.snap similarity index 79% rename from modules/pfr/syri/tests/main.nf.test.snap rename to modules/gallvp/syri/tests/main.nf.test.snap index 8d09bf33..dd39565b 100644 --- a/modules/pfr/syri/tests/main.nf.test.snap +++ b/modules/gallvp/syri/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ], "2": [ - "versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0" + "versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6" ], "error": [ @@ -28,15 +28,15 @@ ] ], "versions": [ - "versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0" + "versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-05-25T21:30:50.653501" + "timestamp": "2024-07-22T14:11:06.589243" }, "homo_sapiens - genome - stub": { "content": [ @@ -53,7 +53,7 @@ ], "2": [ - "versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0" + "versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6" ], "error": [ @@ -67,14 +67,14 @@ ] ], "versions": [ - "versions.yml:md5,05cf55e24c29c2661a2b9301d3c7c2a0" + "versions.yml:md5,0c85b0fa3d80a73807daf08b7e4c51f6" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-05-25T21:22:31.028411" + "timestamp": "2024-07-22T14:11:12.583161" } } \ No newline at end of file diff --git a/modules/pfr/syri/tests/nextflow.config b/modules/gallvp/syri/tests/nextflow.config similarity index 100% rename from modules/pfr/syri/tests/nextflow.config rename to modules/gallvp/syri/tests/nextflow.config diff --git a/modules/pfr/syri/tests/tags.yml b/modules/pfr/syri/tests/tags.yml deleted file mode 100644 index 3afda524..00000000 --- a/modules/pfr/syri/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -syri: - - "modules/pfr/syri/**" diff --git a/subworkflows/local/fasta_synteny.nf b/subworkflows/local/fasta_synteny.nf index ac3dd0ae..f98d6947 100644 --- a/subworkflows/local/fasta_synteny.nf +++ b/subworkflows/local/fasta_synteny.nf @@ -13,7 +13,7 @@ include { CIRCOS } from '../../modules/local/circos' include { LINEARSYNTENY } from '../../modules/local/linearsynteny' include { CUSTOM_RELABELFASTA } from '../../modules/pfr/custom/relabelfasta/main' include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main' -include { SYRI } from '../../modules/pfr/syri/main' +include { SYRI } from '../../modules/gallvp/syri/main' include { PLOTSR } from '../../modules/pfr/plotsr/main' workflow FASTA_SYNTENY {