From 249c2a9b3c601b3f2b6fd8cdcd328b4b3b9c1347 Mon Sep 17 00:00:00 2001 From: Regina Reynolds Date: Mon, 20 Nov 2023 18:28:20 +0000 Subject: [PATCH 1/5] fix: remove GTF_FILTER.out.versions --- subworkflows/local/prepare_genome/main.nf | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 0be947954..0840c7734 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -47,7 +47,7 @@ workflow PREPARE_GENOME { rsem_index // directory: /path/to/rsem/index/ salmon_index // directory: /path/to/salmon/index/ kallisto_index // directory: /path/to/kallisto/index/ - hisat2_index // directory: /path/to/hisat2/index/ + hisat2_index // directory: /path/to/hisat2/index/ bbsplit_index // directory: /path/to/rsem/index/ gencode // boolean: whether the genome is from GENCODE is_aws_igenome // boolean: whether the genome files are from AWS iGenomes @@ -139,14 +139,13 @@ workflow PREPARE_GENOME { } else { ch_transcript_fasta = Channel.value(file(transcript_fasta)) } - if (gencode) { + if (gencode) { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE ( ch_transcript_fasta ) ch_transcript_fasta = PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.fasta ch_versions = ch_versions.mix(PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.versions) } } else { ch_transcript_fasta = MAKE_TRANSCRIPTS_FASTA ( ch_fasta, ch_gtf ).transcript_fasta - ch_versions = ch_versions.mix(GTF_FILTER.out.versions) ch_versions = ch_versions.mix(MAKE_TRANSCRIPTS_FASTA.out.versions) } @@ -268,7 +267,7 @@ workflow PREPARE_GENOME { ch_versions = ch_versions.mix(SALMON_INDEX.out.versions) } } - + // // Uncompress Kallisto index or generate from scratch if required // From 5c50f7d8209a77f1b38c9f80c93add7ba58584ec Mon Sep 17 00:00:00 2001 From: Regina Reynolds Date: Mon, 20 Nov 2023 18:40:00 +0000 Subject: [PATCH 2/5] docs: update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4680c417a..eb5917a71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements and fixes - [[PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix +- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true (issue [#1125](https://github.com/nf-core/rnaseq/issues/1125)) ## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17 From 1398f5c63921e1c9bf457937308c1737b1c81bfc Mon Sep 17 00:00:00 2001 From: Regina Reynolds Date: Mon, 20 Nov 2023 18:41:16 +0000 Subject: [PATCH 3/5] docs: move update to dev --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index eb5917a71..9f90f2c37 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,12 +3,16 @@ 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). +## dev + +### Enhancements and fixes +- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true (issue [#1125](https://github.com/nf-core/rnaseq/issues/1125)) + ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17 ### Enhancements and fixes - [[PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix -- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true (issue [#1125](https://github.com/nf-core/rnaseq/issues/1125)) ## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17 From 317e2e0206ac2f16f504fddc55553749cbce03a6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 19:01:10 +0000 Subject: [PATCH 4/5] Fix CHANGELOG.md --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9f90f2c37..9cf44327d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,13 +6,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## dev ### Enhancements and fixes -- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true (issue [#1125](https://github.com/nf-core/rnaseq/issues/1125)) +- [PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true +- [#1125](https://github.com/nf-core/rnaseq/issues/1125) - Pipeline fails if transcript_fasta not provided and skip_gtf_filter = true ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17 ### Enhancements and fixes -- [[PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix +- [PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix ## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17 From 5e4293090651589c8705db7be85ad88288fa741e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 20 Nov 2023 19:02:43 +0000 Subject: [PATCH 5/5] [automated] Fix linting with Prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9cf44327d..38d6bfb30 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## dev ### Enhancements and fixes + - [PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true - [#1125](https://github.com/nf-core/rnaseq/issues/1125) - Pipeline fails if transcript_fasta not provided and skip_gtf_filter = true