From a0601bbc5e6f51f4542870b616908e00abbc015f Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 9 Apr 2024 10:46:11 +0200 Subject: [PATCH 1/6] add minid option --- conf/modules.config | 2 +- nextflow.config | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 9f2a4760..07f8cd6c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -102,7 +102,7 @@ process { } withName: BBMAP_ALIGN { - ext.args = "trimreaddescriptions=t pigz=t" + ext.args = { "trimreaddescriptions=t pigz=t minid=${params.bbmap_minid}" } publishDir = [ [ path: { "${params.outdir}/bbmap/bam" }, diff --git a/nextflow.config b/nextflow.config index 4d359878..799d9ef2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -47,6 +47,7 @@ params { // Mapping options save_samtools = false save_bam = false + bbmap_minid = 0.9 // orf caller options orf_caller = 'prodigal' From 98fc388e4369ff4ab9827772352eeb5d45f18706 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 9 Apr 2024 10:51:11 +0200 Subject: [PATCH 2/6] update schema.json --- nextflow_schema.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 8f3e0d37..93040fb7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -212,6 +212,13 @@ "save_samtools": { "type": "boolean", "description": "Save the output from samtools" + }, + "bbmap_minid": { + "type": "number", + "default": 0.9, + "fa_icon": "fas fa-address-card", + "description": "Minimum identity needed to assign read to a contig", + "help_text": "" } }, "fa_icon": "fas fa-filter" From 78db663063ff83c6a5e815419d3317f893b1c62a Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 9 Apr 2024 11:32:36 +0200 Subject: [PATCH 3/6] changelog update --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e4dc4679..e0beb187 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,10 +3,10 @@ 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). -## v1.1.0 - [date] +## v1.1.0 - [2024-04-09] ### `Added` - +- [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module - [#271](<[https://github.com/nf-core/metatdenovo/issues/271](https://github.com/nf-core/metatdenovo/issues/271)>) - Added flavor to SPADES modules ### `Changed` From 98cbe3d9d12e2084b85ec39c33bcc4d0b5a792db Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 9 Apr 2024 13:14:29 +0200 Subject: [PATCH 4/6] prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e0beb187..a0e184d1 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 ## v1.1.0 - [2024-04-09] ### `Added` + - [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module - [#271](<[https://github.com/nf-core/metatdenovo/issues/271](https://github.com/nf-core/metatdenovo/issues/271)>) - Added flavor to SPADES modules From 987a3c66791887b6b0ede0ae94c340116ec60fc0 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 9 Apr 2024 13:34:58 +0200 Subject: [PATCH 5/6] bump-version --- CHANGELOG.md | 4 ++-- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a0e184d1..d228fdcf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,11 +3,11 @@ 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). -## v1.1.0 - [2024-04-09] +## v1.1.0dev - [date] ### `Added` -- [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module +- [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module: now the threshold for assing a read is an identity 90%. the previous version of nf-core/metatdenovo was a default of 76%. The user will be always able to change this parameter - [#271](<[https://github.com/nf-core/metatdenovo/issues/271](https://github.com/nf-core/metatdenovo/issues/271)>) - Added flavor to SPADES modules ### `Changed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 03bba2c7..7dbbeab5 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/metatdenovo + This report has been generated by the nf-core/metatdenovo analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-metatdenovo-methods-description": diff --git a/nextflow.config b/nextflow.config index 799d9ef2..fdfbd20c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -291,7 +291,7 @@ manifest { description = """Assembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.0.1' + version = '1.1.0dev' doi = '' } From 02d86731031a9d2967d81478551edfd77929e0a9 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Wed, 10 Apr 2024 09:03:09 +0200 Subject: [PATCH 6/6] Update CHANGELOG.md Co-authored-by: Daniel Lundin --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d228fdcf..85b44295 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module: now the threshold for assing a read is an identity 90%. the previous version of nf-core/metatdenovo was a default of 76%. The user will be always able to change this parameter +- [#280](<[https://github.com/nf-core/metatdenovo/issues/280](https://github.com/nf-core/metatdenovo/issues/280)>) - Added minid option to bbmap_align module. Now the threshold for mapping a read to a contig is an identity of 0.9. The previous version of nf-core/metatdenovo used the default for BBMap, 0.76. This version might hence give slightly different results than the previous. - [#271](<[https://github.com/nf-core/metatdenovo/issues/271](https://github.com/nf-core/metatdenovo/issues/271)>) - Added flavor to SPADES modules ### `Changed`