From 79a493df41ec59698ada96971d1b00d4e0458dbd Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 10:37:13 +0200 Subject: [PATCH 1/6] bump version 2.3.1dev --- CHANGELOG.md | 12 ++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 206091d..49a3cdb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ 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). +## v2.3.1dev nf-core/bacass: "Navy Iron Oyster" + +### `Changed` + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## v2.3.0 nf-core/bacass: "Navy Iron Oyster" 2024/06/12 ### `Changed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index cae0cb1..e647ad5 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/bacass + This report has been generated by the nf-core/bacass analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-bacass-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 03038c3..d27f634 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,7 +278,7 @@ manifest { description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3.0' + version = '2.3.1dev' doi = '10.5281/zenodo.2669428' } From 6008fe50f3c048aa7c7a75a1606c54d41cb72735 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 11:26:17 +0200 Subject: [PATCH 2/6] fix input file not a valid path --- workflows/bacass.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 3ed2de6..6231892 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -95,9 +95,9 @@ workflow BACASS { // def criteria = multiMapCriteria { meta, fastq_1, fastq_2, long_fastq, fast5 -> - shortreads: fastq_1 != 'NA' ? tuple(meta, [fastq_1, fastq_2]) : null - longreads: long_fastq != 'NA' ? tuple(meta, long_fastq) : null - fast5: fast5 != 'NA' ? tuple(meta, fast5) : null + shortreads: fastq_1 != 'NA' ? tuple(meta, [file(fastq_1), file(fastq_2)]) : null + longreads: long_fastq != 'NA' ? tuple(meta, file(long_fastq)) : null + fast5: fast5 != 'NA' ? tuple(meta, file(fast5)) : null } // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ ch_samplesheet From 33b7eab0554265b1e970d0b21a12ecb0168ea0bd Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 11:32:23 +0200 Subject: [PATCH 3/6] update changelog #147 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49a3cdb..4bd4b9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#147](https://github.com/nf-core/bacass/pull/147) Fixed input file errors related to samplesheets containing relative paths to symbolic links, addressing the 'not a valid path' error. + ### `Dependencies` ### `Deprecated` From 621a75062b2b2ba95d3cdab99a20096dc8c2a302 Mon Sep 17 00:00:00 2001 From: Daniel VM <69470278+Daniel-VM@users.noreply.github.com> Date: Fri, 21 Jun 2024 11:59:45 +0200 Subject: [PATCH 4/6] Add reviewer suggestion #147 Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> --- workflows/bacass.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 6231892..f3626c0 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -95,7 +95,7 @@ workflow BACASS { // def criteria = multiMapCriteria { meta, fastq_1, fastq_2, long_fastq, fast5 -> - shortreads: fastq_1 != 'NA' ? tuple(meta, [file(fastq_1), file(fastq_2)]) : null + shortreads: fastq_1 != 'NA' ? tuple(meta, [file(fastq_1, checkIfExists: true), file(fastq_2, checkIfExists: true)]) : null longreads: long_fastq != 'NA' ? tuple(meta, file(long_fastq)) : null fast5: fast5 != 'NA' ? tuple(meta, file(fast5)) : null } From b780766bba6f93b016b87b7e4a17831eb44c3c9c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 21 Jun 2024 12:04:21 +0200 Subject: [PATCH 5/6] extend reviewer suggestion #147 to remaining input files --- workflows/bacass.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index f3626c0..448d0cb 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -96,8 +96,8 @@ workflow BACASS { def criteria = multiMapCriteria { meta, fastq_1, fastq_2, long_fastq, fast5 -> shortreads: fastq_1 != 'NA' ? tuple(meta, [file(fastq_1, checkIfExists: true), file(fastq_2, checkIfExists: true)]) : null - longreads: long_fastq != 'NA' ? tuple(meta, file(long_fastq)) : null - fast5: fast5 != 'NA' ? tuple(meta, file(fast5)) : null + longreads: long_fastq != 'NA' ? tuple(meta, file(long_fastq, checkIfExists: true)) : null + fast5: fast5 != 'NA' ? tuple(meta, file(fast5, checkIfExists: true)) : null } // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ ch_samplesheet From 2c711d12748319e00e754d08abe771418d519a2e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 24 Jun 2024 09:52:10 +0200 Subject: [PATCH 6/6] bump version 2.3.1 --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4bd4b9b..4d476ac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v2.3.1dev nf-core/bacass: "Navy Iron Oyster" +## v2.3.1 nf-core/bacass: "Navy Iron Oyster" 2024/06/24 ### `Changed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e647ad5..95b5ae9 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/bacass + This report has been generated by the nf-core/bacass analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-bacass-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index d27f634..3935924 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,7 +278,7 @@ manifest { description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3.1dev' + version = '2.3.1' doi = '10.5281/zenodo.2669428' }