From 859b542628f3875f4b17e18db21d535c1f0abdd1 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 15 Feb 2023 17:37:33 +0100 Subject: [PATCH 1/3] CHANGELOG.md entry for 1.0.0 --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 13498fc..b8ac96c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,10 +3,12 @@ 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). -## v1.0dev - [date] +## Version 1.0 - [2023-02-15] Initial release of nf-core/phyloplace, created with the [nf-core](https://nf-co.re/) template. +The pipeline performs phylogenetic placement of nucleotide or amino acid sequences in a reference phylogeny. + ### `Added` ### `Fixed` From a93326f28096840bc13d868d491722f7c066d6e6 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 15 Feb 2023 17:37:47 +0100 Subject: [PATCH 2/3] Move metro map to README.md --- README.md | 4 ++++ docs/usage.md | 4 ---- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 2ad8d6e..b0bb9cc 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,10 @@ This ensures that the pipeline runs on AWS, has sensible resource allocation def 3. Graft query sequences onto the reference phylogeny with [`GAPPA`](https://github.com/lczech/gappa). 4. If provided with a classification of the reference sequences, classify query sequences with [`GAPPA`](https://github.com/lczech/gappa). +

+ nf-core/phyloplace workflow overview +

+ ## Quick Start 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) diff --git a/docs/usage.md b/docs/usage.md index 6b5fe5d..a5b6540 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,10 +6,6 @@ ## Introduction -

- nf-core/phyloplace workflow overview -

- This pipeline performs "phylogenetic placement" of query sequences on to a reference phylogeny. With this method, the likelihoods of placing query sequences in the reference phylogeny are calculated on a one-by-one basis. This means that a full phylogeny is not estimated, which is perfect e.g. when sequences come from PCR amplicons or are fragments from metagenomes, but also when the number of query sequences is very large. From 2f90a14e6794d6c44a62d8ccb8c1b4030313151d Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 15 Feb 2023 17:41:56 +0100 Subject: [PATCH 3/3] Updated multiqc module --- modules.json | 2 +- modules/nf-core/multiqc/main.nf | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules.json b/modules.json index a13f58b..fecd482 100644 --- a/modules.json +++ b/modules.json @@ -62,7 +62,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba", "installed_by": ["modules"] } } diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 68f66be..4b60474 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*"