From 0ab9d7ac89c8aeef322063b94c5d38cb0a195a3c Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 14 Jun 2022 10:53:00 +0200 Subject: [PATCH 1/9] Post releas everison bump and CHANGELOG update --- CHANGELOG.md | 10 ++++++++++ nextflow.config | 2 +- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c25942bd..9a3805d4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +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 + +### `Added` + +### `Changed` + +### `Fixed` + +### `Dependencies` + ## v2.2.0 - 2022/06/14 ### `Added` diff --git a/nextflow.config b/nextflow.config index 43926a05..53d81606 100644 --- a/nextflow.config +++ b/nextflow.config @@ -267,7 +267,7 @@ manifest { description = 'Assembly, binning and annotation of metagenomes' mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' - version = '2.2.0' + version = '2.3.0dev' } // Load modules.config for DSL2 module specific options From 7b173b74f85e47c99e4cf9bc4a7f34db06ebaa22 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 24 Jun 2022 10:57:24 +0100 Subject: [PATCH 2/9] Update nextflow_schema.json --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 9cdaf1ec..2af80722 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -14,6 +14,7 @@ "properties": { "input": { "type": "string", + "mimetype": "text/csv", "format": "file-path", "description": "Input FastQ files or CSV samplesheet file containing information about the samples in the experiment.", "help_text": "Use this to specify the location of your input FastQ files. For example:\n\n```bash\n--input 'path/to/data/sample_*_{1,2}.fastq.gz'\n``` \n\nAlternatively, to assign different groups or to include long reads for hybrid assembly with metaSPAdes, you can specify a CSV samplesheet input file with 5 columns and the following header: sample,group,short_reads_1,short_reads_2,long_reads. See [usage docs](https://nf-co.re/mag/usage#input-specifications).", From 285abddbf4595075dd3f2a13d61ed25e3035abf8 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 23 Aug 2022 14:17:56 +0200 Subject: [PATCH 3/9] Fix convert depths gzip issue as reported in https://github.com/nf-core/mag/issues/327 --- CHANGELOG.md | 2 ++ modules/local/convert_depths.nf | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a3805d4..baa55b87 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` +- Fix too many symbolic links issue in local convert_depths module + ### `Dependencies` ## v2.2.0 - 2022/06/14 diff --git a/modules/local/convert_depths.nf b/modules/local/convert_depths.nf index a307f42f..e3c8fb7c 100644 --- a/modules/local/convert_depths.nf +++ b/modules/local/convert_depths.nf @@ -17,7 +17,7 @@ process CONVERT_DEPTHS { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - gunzip $depth + gunzip -f $depth bioawk -t '{ { if (NR > 1) { { print \$1, \$3 } } } }' ${depth.toString() - '.gz'} > ${prefix}_mb2_depth.txt cat <<-END_VERSIONS > versions.yml From a0565342b2d8498a84f8fc635020738e8413d5bb Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Aug 2022 14:19:15 +0200 Subject: [PATCH 4/9] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index baa55b87..465a8e7a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- Fix too many symbolic links issue in local convert_depths module +- [#328](https://github.com/nf-core/mag/pull/328) Fix too many symbolic links issue in local convert_depths module ### `Dependencies` From 1b4456d542367cec093d62ff80d2ced8f65f25fe Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Aug 2022 14:20:12 +0200 Subject: [PATCH 5/9] Fix formatting --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 465a8e7a..d48f2682 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#328](https://github.com/nf-core/mag/pull/328) Fix too many symbolic links issue in local convert_depths module +- [#328](https://github.com/nf-core/mag/pull/328) - Fix too many symbolic links issue in local convert_depths module ### `Dependencies` From 79ac75a8e731a186903a99006361c314fc0c0180 Mon Sep 17 00:00:00 2001 From: Maxime Borry Date: Wed, 24 Aug 2022 11:17:20 +0000 Subject: [PATCH 6/9] add sample name to output directory --- conf/modules.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4051ec08..3739fcff 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -368,7 +368,7 @@ process { withName: PYDAMAGE_ANALYZE { publishDir = [ - path: {"${params.outdir}/Ancient_DNA/pydamage/analyze" }, + path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.id}" }, mode: params.publish_dir_mode ] } @@ -376,7 +376,7 @@ process { withName: PYDAMAGE_FILTER { ext.args = "-t ${params.pydamage_accuracy}" publishDir = [ - path: {"${params.outdir}/Ancient_DNA/pydamage/filter" }, + path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.id}" }, mode: params.publish_dir_mode ] } From 9b26c81358b96c75c6ab0bcbb5e33b79e0f2cba9 Mon Sep 17 00:00:00 2001 From: Maxime Borry Date: Wed, 24 Aug 2022 11:49:03 +0000 Subject: [PATCH 7/9] update changelog [skip ci] --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a3805d4..5a38fd2b 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` +- [#329](https://github.com/nf-core/mag/pull/329) Each sample now gets it's own result directory for PyDamage analysis and filter + ### `Dependencies` ## v2.2.0 - 2022/06/14 From 1414141c383f0e9c37cb76e5101d30fe670b6183 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 25 Aug 2022 09:14:10 +0200 Subject: [PATCH 8/9] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 694702cd..716732d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#328](https://github.com/nf-core/mag/pull/328) - Fix too many symbolic links issue in local convert_depths module -- [#329](https://github.com/nf-core/mag/pull/329) Each sample now gets it's own result directory for PyDamage analysis and filter +- [#329](https://github.com/nf-core/mag/pull/329) - Each sample now gets it's own result directory for PyDamage analysis and filter ### `Dependencies` From 6d794a44aa342903c0eb6f65aae00e640266c31d Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 25 Aug 2022 10:11:54 +0200 Subject: [PATCH 9/9] Bump version and update changelog --- CHANGELOG.md | 6 +++--- nextflow.config | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 716732d6..86d63d74 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). -## dev +## v2.2.1 - 2022/08/25 ### `Added` @@ -11,8 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#328](https://github.com/nf-core/mag/pull/328) - Fix too many symbolic links issue in local convert_depths module -- [#329](https://github.com/nf-core/mag/pull/329) - Each sample now gets it's own result directory for PyDamage analysis and filter +- [#328](https://github.com/nf-core/mag/pull/328) - Fix too many symbolic links issue in local convert_depths module (reported by @ChristophKnapp and fixed by @apeltzer, @jfy133) +- [#329](https://github.com/nf-core/mag/pull/329) - Each sample now gets it's own result directory for PyDamage analysis and filter (reported and fixed by @maxibor) ### `Dependencies` diff --git a/nextflow.config b/nextflow.config index 53d81606..11854378 100644 --- a/nextflow.config +++ b/nextflow.config @@ -267,7 +267,7 @@ manifest { description = 'Assembly, binning and annotation of metagenomes' mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' - version = '2.3.0dev' + version = '2.2.1' } // Load modules.config for DSL2 module specific options