From 3f07b0fde2e773119d12c24266f008435459857d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 09:31:03 +0200 Subject: [PATCH 1/3] fix usage of fasta references --- subworkflows/local/prepare_genome.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 02a983d1..16d02aa6 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -64,7 +64,7 @@ workflow PREPARE_GENOME { if (params.fasta_index) { ch_fasta_index = Channel.value(file(params.fasta_index)) } else { - SAMTOOLS_FAIDX([[:], ch_fasta]) + SAMTOOLS_FAIDX(ch_fasta.map{ fasta -> [[:], fasta]}) ch_fasta_index = SAMTOOLS_FAIDX.out.fai.map{ return(it[1])} ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) } From e72476b6e537e91535eb251ef367843f3bf61ef0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 09:58:24 +0200 Subject: [PATCH 2/3] update contributors --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index ba94d5a0..7f755833 100644 --- a/README.md +++ b/README.md @@ -96,6 +96,7 @@ These scripts were originally written for use at the [National Genomics Infrastr - Rickard Hammarรฉn ([@Hammarn](https://github.com/Hammarn/)) - Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/)) - Patrick Hรผther ([@phue](https://github.com/phue/)) + - Maxime U Garica ([@maxulysse](https://github.com/maxulysse/)) ## Contributions and Support From d38c4b186352dc02acac8fbc76b12c8b5c371a0f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 10:06:47 +0200 Subject: [PATCH 3/3] update CHANGELOG --- CHANGELOG.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cf494fdd..51a41809 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,15 @@ ## v2.7.0dev - [date] +### Bug fixes & refactoring + +- ๐Ÿ”„ Updated template to nf-core/tools v2.12 [#377](https://github.com/nf-core/methylseq/pull/377) +- ๐Ÿ”„ Updated template to nf-core/tools v2.13 [#380](https://github.com/nf-core/methylseq/pull/380) +- ๐Ÿ”„ Updated template to nf-core/tools v2.13.1 [#384](https://github.com/nf-core/methylseq/pull/384) +- ๐Ÿ”„ Updated template to nf-core/tools v2.14.1 [#399](https://github.com/nf-core/methylseq/pull/399) +- ๐Ÿ› fix sample/replicate merge [#401](https://github.com/nf-core/methylseq/pull/401) +- ๐Ÿ› fix fasta reference usage [#403](https://github.com/nf-core/methylseq/pull/403) + ## [v2.6.0](https://github.com/nf-core/methylseq/releases/tag/2.6.0) - 2024-01-05 ### Bug fixes & refactoring