From a3d2690f5298003ea1db26b33bacfe032e96c98d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Guizard?= Date: Mon, 13 Mar 2023 10:50:50 +0000 Subject: [PATCH 1/4] FIX: Do not run SET_GTF_CHANNEL with minimap2 path --- workflows/isoseq.nf | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/workflows/isoseq.nf b/workflows/isoseq.nf index bc6b218..e306730 100644 --- a/workflows/isoseq.nf +++ b/workflows/isoseq.nf @@ -93,12 +93,13 @@ workflow ISOSEQ { // INPUT_CHECK(file(params.input), params.chunk) // Check samplesheet input for PBCCS module ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - - SET_CHUNK_NUM_CHANNEL(params.input, params.chunk) // Prepare channels for: + // Prepare channels for: + SET_CHUNK_NUM_CHANNEL(params.input, params.chunk) // - PBCCS parallelization SET_FASTA_CHANNEL(params.fasta) // - genome fasta - SET_GTF_CHANNEL(params.gtf) // - primers fasta - SET_PRIMERS_CHANNEL(params.primers) // - genome gtf - // - PBCCS parallelization + SET_PRIMERS_CHANNEL(params.primers) // - primers fasta + if (params.aligner == "ultra") { + SET_GTF_CHANNEL(params.gtf) // - genome gtf + } PBCCS(INPUT_CHECK.out.reads, SET_CHUNK_NUM_CHANNEL.out.chunk_num, params.chunk) // Generate CCS from raw reads PBCCS.out.bam // Update meta: update id (+chunkX) and store former id From 8a2c61ddd9a1c43c3454e95aa6377840e457c2d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Guizard?= Date: Mon, 13 Mar 2023 11:03:30 +0000 Subject: [PATCH 2/4] Don't set up gtf option for minimap2 path --- conf/test_minimap2.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/test_minimap2.config b/conf/test_minimap2.config index f33dabd..fe07514 100644 --- a/conf/test_minimap2.config +++ b/conf/test_minimap2.config @@ -23,7 +23,6 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/samplesheet.csv' primers = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/primers.fasta' fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' - gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.104.chr.13_18_19.gtf' rq = 0.9 chunk = 5 five_prime = 100 From 74a511b3e7ee505023af0af377c3258bd04c2406 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Guizard?= Date: Mon, 13 Mar 2023 11:30:31 +0000 Subject: [PATCH 3/4] Update CHANGELOG.md --- CHANGELOG.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index dac59b8..682a914 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,20 @@ 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). + +## v1.1.4 - Teal Albatross [13/03/2023] + +### `Added` + +### `Fixed` + +- Update minimap2 path test: Don't set gtf option. It is not expected to be used with minimap2 is chosen. +- FIX: Don't prepare gtf channel when minimap2 is chosen. + +### `Dependencies` + +### `Deprecated` + ## v1.1.3 - Blue Grouse [06/03/2023] ### `Added` From 3ccf5f83180d57470a66062e545f31aedb6017d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Guizard?= Date: Mon, 13 Mar 2023 11:48:17 +0000 Subject: [PATCH 4/4] Prettier --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 682a914..506cf7f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,6 @@ 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). - ## v1.1.4 - Teal Albatross [13/03/2023] ### `Added`