From a722f7fe3755fb597226e9732bd541997511b5e9 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Fri, 15 Mar 2024 10:01:47 +0100 Subject: [PATCH 1/8] bump to 1.2.0dev --- CHANGELOG.md | 2 ++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 27150aa2..3531d49f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 1.2.0dev - canguro + ## 1.1.1 - LATÜRNICH This release fixes some important bugs: diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c6b56005..e3d29f8d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/pangenome + This report has been generated by the nf-core/pangenome analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-pangenome-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index ec06325d..d0d726c7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -277,7 +277,7 @@ manifest { description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.1' + version = '1.2.0dev' doi = 'https://doi.org/10.5281/zenodo.8202636' } From c600a43fd6b27f35ef3b8f6c24385223bd490c31 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Mon, 25 Mar 2024 14:22:43 +0100 Subject: [PATCH 2/8] revert wfmash to v0.10.4 --- conf/modules.config | 24 ++++++------ modules.json | 2 +- modules/nf-core/wfmash/environment.yml | 7 ---- modules/nf-core/wfmash/main.nf | 6 +-- modules/nf-core/wfmash/meta.yml | 7 ++-- modules/nf-core/wfmash/tests/main.nf.test | 39 ------------------- .../nf-core/wfmash/tests/main.nf.test.snap | 33 ---------------- modules/nf-core/wfmash/tests/nextflow.config | 12 ------ modules/nf-core/wfmash/tests/tags.yml | 2 - nextflow.config | 2 +- nextflow_schema.json | 4 +- 11 files changed, 23 insertions(+), 115 deletions(-) delete mode 100644 modules/nf-core/wfmash/environment.yml delete mode 100644 modules/nf-core/wfmash/tests/main.nf.test delete mode 100644 modules/nf-core/wfmash/tests/main.nf.test.snap delete mode 100644 modules/nf-core/wfmash/tests/nextflow.config delete mode 100644 modules/nf-core/wfmash/tests/tags.yml diff --git a/conf/modules.config b/conf/modules.config index c5dc2c4e..b4dcdf32 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -102,7 +102,7 @@ process { withName: WFMASH_MAP_ALIGN { ext.args = { [ - "-n ${params.wfmash_n_mappings}", + params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -113,8 +113,8 @@ process { "-H ${params.wfmash_mash_kmer_thres}", "${wfmash_sparse_map_cmd}", params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", - "-2 ${params.wfmash_hg_filter_ani_diff}", - "--lower-triangular", +// "-2 ${params.wfmash_hg_filter_ani_diff}", +// "--lower-triangular", ].join(" ").trim() } publishDir = [ @@ -127,7 +127,7 @@ process { withName: WFMASH_MAP { ext.args = { [ - "-n ${params.wfmash_n_mappings}", + params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -139,8 +139,8 @@ process { "${wfmash_sparse_map_cmd}", params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", "-m", - "-2 ${params.wfmash_hg_filter_ani_diff}", - "--lower-triangular", +// "-2 ${params.wfmash_hg_filter_ani_diff}", +// "--lower-triangular", ].join(" ").trim() } publishDir = [ @@ -153,7 +153,7 @@ process { withName: WFMASH_MAP_COMMUNITY { ext.args = { [ - "-n ${params.wfmash_n_mappings}", + params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -165,8 +165,8 @@ process { "${wfmash_sparse_map_cmd}", params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", "-m", - "-2 ${params.wfmash_hg_filter_ani_diff}", - "--lower-triangular", +// "-2 ${params.wfmash_hg_filter_ani_diff}", +// "--lower-triangular", ].join(" ").trim() } publishDir = [ @@ -188,7 +188,7 @@ process { withName: WFMASH_ALIGN { ext.args = { [ - "-n ${params.wfmash_n_mappings}", + params.wfmash_n_mappings ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}", "-s ${parse_int(params.wfmash_segment_length)}", "-p ${params.wfmash_map_pct_id}", params.wfmash_merge_segments ? "-M" : "", @@ -200,8 +200,8 @@ process { "${wfmash_sparse_map_cmd}", params.wfmash_temp_dir ? "-B ${wfmash_temp_dir}" : "", "--invert-filtering", - "-2 ${params.wfmash_hg_filter_ani_diff}", - "--lower-triangular", +// "-2 ${params.wfmash_hg_filter_ani_diff}", +// "--lower-triangular", ].join(" ").trim() } publishDir = [ diff --git a/modules.json b/modules.json index eecc70e3..134e8709 100644 --- a/modules.json +++ b/modules.json @@ -82,7 +82,7 @@ }, "wfmash": { "branch": "master", - "git_sha": "0c49f318ec4701b891a87f25fb07b34713c90203", + "git_sha": "77c0c76b7eb7ec564617e635953addc9fb40b61e", "installed_by": ["modules"] } } diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml deleted file mode 100644 index 071aa5a7..00000000 --- a/modules/nf-core/wfmash/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: wfmash -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::wfmash=0.12.6 diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf index 7c64148b..33c556ad 100644 --- a/modules/nf-core/wfmash/main.nf +++ b/modules/nf-core/wfmash/main.nf @@ -2,10 +2,10 @@ process WFMASH { tag "$meta.id" label 'process_medium' - conda "${moduleDir}/environment.yml" + conda "bioconda::wfmash=0.10.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/wfmash:0.12.6--h11f254b_0': - 'biocontainers/wfmash:0.12.6--h11f254b_0' }" + 'https://depot.galaxyproject.org/singularity/wfmash:0.10.4--hea8008d_0': + 'biocontainers/wfmash:0.10.4--hea8008d_0' }" input: tuple val(meta), path(fasta_gz), path(paf), path(gzi), path(fai) diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml index dc5cd5a8..80e630cc 100644 --- a/modules/nf-core/wfmash/meta.yml +++ b/modules/nf-core/wfmash/meta.yml @@ -13,7 +13,8 @@ tools: documentation: https://github.com/waveygang/wfmash tool_dev_url: https://github.com/waveygang/wfmash doi: 10.5281/zenodo.6949373 - licence: ["MIT"] + licence: "['MIT']" + input: - meta: type: map @@ -43,6 +44,7 @@ input: type: file description: Optional inpute file in FASTA format specifying the query sequences as a list. pattern: "*.{fa,fna,fasta}" + output: - meta: type: map @@ -57,7 +59,6 @@ output: type: file description: File containing software versions pattern: "versions.yml" + authors: - "@subwaystation" -maintainers: - - "@subwaystation" diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test deleted file mode 100644 index 41d8c23c..00000000 --- a/modules/nf-core/wfmash/tests/main.nf.test +++ /dev/null @@ -1,39 +0,0 @@ -nextflow_process { - - name "Test Process WFMASH" - script "../main.nf" - process "WFMASH" - config "./nextflow.config" - - tag "modules" - tag "modules_nfcore" - tag "wfmash" - - test("homo_sapiens - pangenome - pangenome_fa_bgzip") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip'], checkIfExists: true), - [], // empty paf input - file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_gzi'], checkIfExists: true), // gzi - file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_fai'], checkIfExists: true) // fai - ] - input[1] = true // empty paf input - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, -// { assert snapshot(process.out).exists() } // if run on more than 1 thread the lines in the resulting PAF will appear in a different order - ) - } - - } - -} diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap deleted file mode 100644 index 97a51e44..00000000 --- a/modules/nf-core/wfmash/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "homo_sapiens - pangenome - pangenome_fa_bgzip": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd" - ] - ], - "1": [ - "versions.yml:md5,0da45b7a6424a967e2f39225fb020140" - ], - "paf": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd" - ] - ], - "versions": [ - "versions.yml:md5,0da45b7a6424a967e2f39225fb020140" - ] - } - ], - "timestamp": "2024-01-25T15:12:21.284828212" - } -} \ No newline at end of file diff --git a/modules/nf-core/wfmash/tests/nextflow.config b/modules/nf-core/wfmash/tests/nextflow.config deleted file mode 100644 index b7e9c989..00000000 --- a/modules/nf-core/wfmash/tests/nextflow.config +++ /dev/null @@ -1,12 +0,0 @@ -process { - - withName: WFMASH { - ext.args = { - [ - "-s 500", // necessary because of https://github.com/waveygang/wfmash/issues/218 - "-X" - ].join(" ").trim() - } - } - -} diff --git a/modules/nf-core/wfmash/tests/tags.yml b/modules/nf-core/wfmash/tests/tags.yml deleted file mode 100644 index 7001b087..00000000 --- a/modules/nf-core/wfmash/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -wfmash: - - "modules/nf-core/wfmash/**" diff --git a/nextflow.config b/nextflow.config index d0d726c7..9782b3f4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,7 +27,7 @@ params { wfmash_only = false wfmash_temp_dir = null wfmash_hg_filter_ani_diff = 30 - wfmash_n_mappings = 1 + wfmash_n_mappings = null // Seqwish options seqwish_paf = null diff --git a/nextflow_schema.json b/nextflow_schema.json index ab4f48d7..ddd643d2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -122,8 +122,8 @@ }, "wfmash_n_mappings": { "type": "integer", - "default": 1, - "description": "Number of mappings for each segment." + "default": null, + "description": "Number of mappings for each segment. [defualt: n_haplotypes - 1]." } } }, From d08c989af7f37214eb625f8b373e579377ceea8f Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Mon, 25 Mar 2024 15:01:52 +0100 Subject: [PATCH 3/8] Update nextflow_schema.json Co-authored-by: Phil Ewels --- nextflow_schema.json | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index ddd643d2..274f1e52 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -122,7 +122,6 @@ }, "wfmash_n_mappings": { "type": "integer", - "default": null, "description": "Number of mappings for each segment. [defualt: n_haplotypes - 1]." } } From e9ee0421df471a4ff697ec7cfc36be38f6e87dd5 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Mon, 25 Mar 2024 15:03:24 +0100 Subject: [PATCH 4/8] typo --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 274f1e52..16ad7e0b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -122,7 +122,7 @@ }, "wfmash_n_mappings": { "type": "integer", - "description": "Number of mappings for each segment. [defualt: n_haplotypes - 1]." + "description": "Number of mappings for each segment. [default: n_haplotypes - 1]." } } }, From d593a1ba2d19bbc915e76f515913c1a28a2ce605 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Mon, 25 Mar 2024 15:20:10 +0100 Subject: [PATCH 5/8] bump to 1.1.2 - canguro --- CHANGELOG.md | 8 +++++++- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3531d49f..4a7e9906 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 1.2.0dev - canguro +## 1.1.2 - canguro + +This release reverts the `wfmash` tool version to 0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly. +It is currently unclear, when a new *stable* release will become available. People like @baozg or @AndreaGuarracino are evaluating. + +- Per default, we set the number of mappings in `wfmash` to `--n_haplotypes - 1`. Previously, this was set to `1`. +- Deactivated parameter `wfmash_hg_filter_ani_diff`, because the older `wfmash` version does not support it. ## 1.1.1 - LATÜRNICH diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e3d29f8d..31ab221a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/pangenome + This report has been generated by the nf-core/pangenome analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-pangenome-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 9782b3f4..3d10ac90 100644 --- a/nextflow.config +++ b/nextflow.config @@ -277,7 +277,7 @@ manifest { description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.2.0dev' + version = '1.1.2' doi = 'https://doi.org/10.5281/zenodo.8202636' } From 1f01e2aad9a0712ec3715f599d5c217c7c5d1bd3 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Mar 2024 14:23:15 +0000 Subject: [PATCH 6/8] [automated] Fix code linting --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a7e9906..e85ae5b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) ## 1.1.2 - canguro This release reverts the `wfmash` tool version to 0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly. -It is currently unclear, when a new *stable* release will become available. People like @baozg or @AndreaGuarracino are evaluating. +It is currently unclear, when a new _stable_ release will become available. People like @baozg or @AndreaGuarracino are evaluating. - Per default, we set the number of mappings in `wfmash` to `--n_haplotypes - 1`. Previously, this was set to `1`. - Deactivated parameter `wfmash_hg_filter_ani_diff`, because the older `wfmash` version does not support it. From dbcd775487253892c42bc1c6ae6f5e2758420b98 Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Mon, 25 Mar 2024 15:50:25 +0100 Subject: [PATCH 7/8] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e85ae5b0..e9a045c0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) ## 1.1.2 - canguro This release reverts the `wfmash` tool version to 0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly. -It is currently unclear, when a new _stable_ release will become available. People like @baozg or @AndreaGuarracino are evaluating. +It is currently unclear, when a new _stable_ release will become available. @baozg or @AndreaGuarracino are evaluating. - Per default, we set the number of mappings in `wfmash` to `--n_haplotypes - 1`. Previously, this was set to `1`. - Deactivated parameter `wfmash_hg_filter_ani_diff`, because the older `wfmash` version does not support it. From 9b4a2cac79af9a7a91f576d0297f3e7891f2bc1b Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Mon, 25 Mar 2024 15:51:09 +0100 Subject: [PATCH 8/8] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 16ad7e0b..38238b73 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -122,7 +122,7 @@ }, "wfmash_n_mappings": { "type": "integer", - "description": "Number of mappings for each segment. [default: n_haplotypes - 1]." + "description": "Number of mappings for each segment. [default: `n_haplotypes - 1`]." } } },