From 9106f73dbbfba241e7aaecf9dd7aa9d280c199fe Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Tue, 12 Mar 2024 18:02:34 +0100 Subject: [PATCH 1/6] switch to nextclade 3 - adapt how to get the dataset tag - check for nextclade 3 with --update --- CoVpipe2.nf | 4 ++-- modules/nextclade.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CoVpipe2.nf b/CoVpipe2.nf index 2d72d1d..e7ab5ac 100644 --- a/CoVpipe2.nf +++ b/CoVpipe2.nf @@ -172,8 +172,8 @@ if ( workflow.containerEngine && params.update ) { params.pangolin_docker = "rkimf1/pangolin:" + tagname println "\033[0;32mFound latest pangolin container, using: " + params.pangolin_docker + " \033[0m" - tagname = 'https://registry.hub.docker.com/v2/repositories/rkimf1/nextclade2/tags/'.toURL().text.split(',"name":"')[1].split('","')[0] - params.nextclade_docker = "rkimf1/nextclade2:" + tagname + tagname = 'https://registry.hub.docker.com/v2/repositories/rkimf1/nextclade3/tags/'.toURL().text.split(',"name":"')[1].split('","')[0] + params.nextclade_docker = "rkimf1/nextclade3:" + tagname println "\033[0;32mFound latest nextclade container, using: " + params.nextclade_docker + " \033[0m" } if ( internetcheck.toString() == "false" ) { diff --git a/modules/nextclade.nf b/modules/nextclade.nf index 728294c..5f3af58 100644 --- a/modules/nextclade.nf +++ b/modules/nextclade.nf @@ -25,7 +25,7 @@ process nextclade { cat tmp.tsv | tr -d "\r" > ${name}_clade.tsv used_nextclade_version=\$nextclade_version_curr - used_nextcladedataset_tag=\$(grep -Po '"tag":.*' data/${nextclade_dataset_name}/tag.json | cut -d' ' -f 2 | tr -d '"') + used_nextcladedataset_tag=\$(grep -Po '"tag":.*' data/${nextclade_dataset_name}/pathogen.json | cut -d' ' -f 2 | tr -d '"' | tr -d ',') used_nextcladedataset_info="${nextclade_dataset_name}, \$used_nextcladedataset_tag" """ stub: From 40041720cfa300f0479d8b2802d681b6c54876e9 Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Tue, 12 Mar 2024 18:03:42 +0100 Subject: [PATCH 2/6] bump pangolin and nextclade - pangolin=4.3, pangolin-data=1.25.1 - nextclade=3.3.1 --- nextflow.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index 0d23555..fd30bbc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -74,12 +74,12 @@ params { // update settings and default container update = false - pangolin_docker_default = 'rkimf1/pangolin:4.2-1.18.1.1--e24af6d' - nextclade_docker_default = 'rkimf1/nextclade2:2.13.1--ddb9e60' - pangolin_conda_default = 'bioconda::pangolin=4.2 bioconda::pangolin-data=1.18.1.1' - nextclade_conda_default = 'bioconda::nextclade=2.13.1' + pangolin_docker_default = 'rkimf1/pangolin-4.3-1.25.1--380d5e9' + nextclade_docker_default = 'rkimf1/nextclade3:3.3.1--c7323e6' + pangolin_conda_default = 'bioconda::pangolin=4.3 bioconda::pangolin-data=1.25.1' + nextclade_conda_default = 'bioconda::nextclade=3.3.1' nextclade_dataset_name = 'sars-cov-2' - nextclade_dataset_tag = '2023-04-18T12:00:00Z' + nextclade_dataset_tag = '2024-02-16--04-00-32Z' // output folder structure output = 'results' From 2dc68241f1b084d172b35f162c3b567cfa10d10b Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Wed, 13 Mar 2024 09:00:40 +0100 Subject: [PATCH 3/6] fixed default pangolin docker name --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index fd30bbc..0afc2a9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -74,7 +74,7 @@ params { // update settings and default container update = false - pangolin_docker_default = 'rkimf1/pangolin-4.3-1.25.1--380d5e9' + pangolin_docker_default = 'rkimf1/pangolin:4.3-1.25.1--380d5e9' nextclade_docker_default = 'rkimf1/nextclade3:3.3.1--c7323e6' pangolin_conda_default = 'bioconda::pangolin=4.3 bioconda::pangolin-data=1.25.1' nextclade_conda_default = 'bioconda::nextclade=3.3.1' From 2e0b95cc6d99d58d30b3a532595acfbcd6e96f82 Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Wed, 13 Mar 2024 09:54:29 +0100 Subject: [PATCH 4/6] updated md5sum for pangolin output - default pangolin version changed --- tests/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test.yml b/tests/test.yml index ded7d2e..669010c 100644 --- a/tests/test.yml +++ b/tests/test.yml @@ -129,7 +129,7 @@ - path: "results/Report/single_tables/nextclade_results.tsv" md5sum: 58b42101676f5fab5d82c94b8dd91671 - path: "results/Report/single_tables/pangolin_results.csv" - md5sum: df49cfb48015c8df2ce402aac0ce7a98 + md5sum: fcf7e3bc0b3c852a08a8ba801c406920 - path: "results/Report/single_tables/president_results.tsv" - path: "results/Report/single_tables/sc2rf_results.csv" md5sum: d02d8ab1b54d11b1aa16edc719b75796 From 063dc7486822d7e240d9f2efc54e570052d1aad7 Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Wed, 13 Mar 2024 10:15:31 +0100 Subject: [PATCH 5/6] updated nextclade output --- tests/test.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/test.yml b/tests/test.yml index 669010c..de502d8 100644 --- a/tests/test.yml +++ b/tests/test.yml @@ -100,14 +100,14 @@ - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE.aligned.fasta" md5sum: 59ee3f944dcda28f16c20f00a819aa0e - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_clade.tsv" - md5sum: 6cdd6ae28611b295d06594993f8ab3bc + md5sum: 92f74146db907b4c8086ccbb550953c8 - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_lineage_report.csv" contains: - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note" - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE.aligned.fasta" md5sum: e1936924ec8fe26dbc87a2277e4a3dac - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_clade.tsv" - md5sum: ac2e403922170a07a41a48947b768a12 + md5sum: aa9ff26b8308444690ce986dfe7bed59 - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_lineage_report.csv" contains: - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note" @@ -127,7 +127,7 @@ md5sum: b649f9400fe6842b2f8a2537e137f66a - path: "results/Report/report_datatable.xlsx" - path: "results/Report/single_tables/nextclade_results.tsv" - md5sum: 58b42101676f5fab5d82c94b8dd91671 + md5sum: 7823b5b56e31a5412263384f10d7f204 - path: "results/Report/single_tables/pangolin_results.csv" md5sum: fcf7e3bc0b3c852a08a8ba801c406920 - path: "results/Report/single_tables/president_results.tsv" @@ -236,14 +236,14 @@ - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE.aligned.fasta" md5sum: 59ee3f944dcda28f16c20f00a819aa0e - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_clade.tsv" - md5sum: a4ac4a5a69067232f1d9919a45f9ecab + md5sum: 92f74146db907b4c8086ccbb550953c8 - path: "results/05-Linages_Mutations/SAMPLE1_PE/SAMPLE1_PE_lineage_report.csv" contains: - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note" - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE.aligned.fasta" md5sum: e1936924ec8fe26dbc87a2277e4a3dac - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_clade.tsv" - md5sum: a8bd3d4e09ae750f07ae6cd5d8a83def + md5sum: aa9ff26b8308444690ce986dfe7bed59 - path: "results/05-Linages_Mutations/SAMPLE2_PE/SAMPLE2_PE_lineage_report.csv" contains: - "taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note" @@ -263,7 +263,7 @@ md5sum: b649f9400fe6842b2f8a2537e137f66a - path: "results/Report/report_datatable.xlsx" - path: "results/Report/single_tables/nextclade_results.tsv" - md5sum: dc7a07bc062837349d151c8946ae29c2 + md5sum: 7823b5b56e31a5412263384f10d7f204 - path: "results/Report/single_tables/pangolin_results.csv" - path: "results/Report/single_tables/president_results.tsv" - path: "results/Report/single_tables/sc2rf_results.csv" From bb3a3b3dd972f454187ee8a2a965535352fc054d Mon Sep 17 00:00:00 2001 From: "Lataretu, Marie" Date: Wed, 13 Mar 2024 11:04:56 +0100 Subject: [PATCH 6/6] updated changelog --- CHANGELOG.md | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ddbafe3..353d0f3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,34 @@ All notable changes to this project will be documented in this file. 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). +## [0.5.0] 2024-03-13 + +### Changed + +- updated default `nextclade` version to `3.3.1` + - default dataset version `2024-02-16--04-00-32Z` +- updated default `pangolin` version to `4.3` + - default `pangolin-data` version 1.25.1 + +## [0.4.3] 2023-06-26 + +### Fixed + +- fixed conda channel order +- enhanced nextclade dataset provenance + +## [0.4.2] 2023-06-08 + +### Added + +- added a DOI + +## [0.4.1] 2023-05-23 + +### Changed + +- update documentation + ## [0.4.0] 2023-05-09 ### Added