From fef43ae483bdba267b4209384b7598d2444539a9 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 2 Feb 2024 15:35:12 +0100 Subject: [PATCH 01/15] Post-release version bump --- 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 feb3c137..160167f4 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). +## dev - [unreleased] + +### `Added` + +### `Changed` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## 2.5.2 - [2024-02-02] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index de0b96a6..7eebb4d0 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/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index fd0094b9..c26f9dfd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -379,7 +379,7 @@ manifest { description = """Assembly, binning and annotation of metagenomes""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.2' + version = '2.5.3dev' doi = '10.1093/nargab/lqac007' } From 708fe390c78c0f543eddd22af6cf35f81c7f8235 Mon Sep 17 00:00:00 2001 From: maxibor Date: Fri, 2 Feb 2024 16:32:33 +0100 Subject: [PATCH 02/15] ch_cat_global_summary --- workflows/mag.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/mag.nf b/workflows/mag.nf index 61ce43bc..6ec7b132 100644 --- a/workflows/mag.nf +++ b/workflows/mag.nf @@ -960,7 +960,7 @@ workflow MAG { // If CAT is not run, then the CAT global summary should be an empty channel if ( params.cat_db_generate || params.cat_db) { - ch_cat_global_summary = CAT_SUMMARY.out.summary + ch_cat_global_summary = CAT_SUMMARY.out.combined } else { ch_cat_global_summary = Channel.empty() } From d423f99b8fafcbdba3676cd6f4921280e71016c8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 2 Feb 2024 23:30:24 +0100 Subject: [PATCH 03/15] Temporarily disable GTDB until have latest release --- conf/test_full.config | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index ea694247..dccff384 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -22,12 +22,18 @@ params { centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz" kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz" cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz" - gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r202_data.tar.gz" + // gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" + skip_gtdbtk = true + + // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system + skip_spades = true + skip_spadeshybrid = true // reproducibility options for assembly spades_fix_cpus = 10 spadeshybrid_fix_cpus = 10 megahit_fix_cpu_1 = true + // available options to enable reproducibility for BUSCO (--busco_db) not used here // to allow detection of possible problems in automated lineage selection mode using public databases From 5a7df431b1ed36f8ff822e199c4cf06dfeace655 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 2 Feb 2024 23:35:23 +0100 Subject: [PATCH 04/15] Add missing changelog entry --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 160167f4..36c63747 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` +- [#574](https://github.com/nf-core/mag/pull/574) - Fix wrong channel going to BIN_SUMMARY (fix by @maxibor) + ### `Dependencies` ### `Deprecated` From fa4f841f32a01d21d4eeb68f16b8c81c86ce45ee Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 3 Feb 2024 00:03:09 +0100 Subject: [PATCH 05/15] Deactivate centrfigue because AWS bucket download problems --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index dccff384..d7f3365e 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -19,7 +19,7 @@ params { host_fasta = "s3://ngi-igenomes/test-data/mag/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz" input = "s3://ngi-igenomes/test-data/mag/samplesheets/samplesheet.full.csv" - centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz" + //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz" kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz" cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz" // gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" From ef09854efd206f34e3175936e45711c950baa49c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 3 Feb 2024 21:28:49 +0100 Subject: [PATCH 06/15] Try now with latest GTDB file (note previous commit worked on AWS!) --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index d7f3365e..09328a70 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -23,7 +23,7 @@ params { kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz" cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz" // gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" - skip_gtdbtk = true + skip_gtdbtk = false // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system skip_spades = true From 2921b861212fe5cb99b48beca23c9c26af699d65 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 3 Feb 2024 21:29:09 +0100 Subject: [PATCH 07/15] Uncomment GTDB line --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 09328a70..7036b7c6 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -22,7 +22,7 @@ params { //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz" kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz" cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz" - // gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" + gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" skip_gtdbtk = false // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system From 63cf3577d358a6ffe9874a1fac605cf5176669b8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 4 Feb 2024 09:00:49 +0100 Subject: [PATCH 08/15] deactivate gtdb due to Aws incompatibility --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 7036b7c6..09328a70 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -22,7 +22,7 @@ params { //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz" kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz" cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz" - gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" + // gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" skip_gtdbtk = false // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system From 1504f9c58149de2bcfb5815d9b920c8963432a88 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 4 Feb 2024 09:00:57 +0100 Subject: [PATCH 09/15] Update conf/test_full.config --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 09328a70..d7f3365e 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -23,7 +23,7 @@ params { kraken2_db = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz" cat_db = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz" // gtdb_db = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" - skip_gtdbtk = false + skip_gtdbtk = true // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system skip_spades = true From 818b9b424b43d60b608b51a82978bfaeae0ebb5d Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 08:41:26 +0100 Subject: [PATCH 10/15] Apply suggestions from code review --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 36c63747..c1afaa78 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#575](https://github.com/nf-core/mag/pull/575/files) - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133) + ### `Fixed` - [#574](https://github.com/nf-core/mag/pull/574) - Fix wrong channel going to BIN_SUMMARY (fix by @maxibor) From 2c8a8e45dfaf1989c7ad92e43dba8e47a21e99f8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 08:41:50 +0100 Subject: [PATCH 11/15] Linting --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c1afaa78..9f999a79 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#575](https://github.com/nf-core/mag/pull/575/files) - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133) +- [#575](https://github.com/nf-core/mag/pull/575/files) - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133) ### `Fixed` From 3dad578c76537cbd73d5e964f2e2470c60eeab6c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 08:43:54 +0100 Subject: [PATCH 12/15] Bump versions for patch release --- 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 9f999a79..4923b993 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 - [unreleased] +## 2.5.3 - [2024-02-05] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 7eebb4d0..234d1d8d 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/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index c26f9dfd..6a2da3b5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -379,7 +379,7 @@ manifest { description = """Assembly, binning and annotation of metagenomes""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.3dev' + version = '2.5.3' doi = '10.1093/nargab/lqac007' } From cc0a6fe84539a79309a9c95c567a0bf4e59220d7 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 08:45:14 +0100 Subject: [PATCH 13/15] Revert "Bump versions for patch release" This reverts commit 3dad578c76537cbd73d5e964f2e2470c60eeab6c. --- 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 4923b993..9f999a79 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). -## 2.5.3 - [2024-02-05] +## dev - [unreleased] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 234d1d8d..7eebb4d0 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/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 6a2da3b5..c26f9dfd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -379,7 +379,7 @@ manifest { description = """Assembly, binning and annotation of metagenomes""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.3' + version = '2.5.3dev' doi = '10.1093/nargab/lqac007' } From 2ddccd3f58502bb988c764c89ae9b2e9ed846c23 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 08:46:56 +0100 Subject: [PATCH 14/15] Bump version for patch release --- 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 9f999a79..4923b993 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 - [unreleased] +## 2.5.3 - [2024-02-05] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 7eebb4d0..234d1d8d 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/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index c26f9dfd..6a2da3b5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -379,7 +379,7 @@ manifest { description = """Assembly, binning and annotation of metagenomes""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.3dev' + version = '2.5.3' doi = '10.1093/nargab/lqac007' } From 532a7c780228e50b60d69e24bc6fc5c619dada16 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 15:44:49 +0100 Subject: [PATCH 15/15] Apply suggestions from code review --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4923b993..9e0d2429 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#575](https://github.com/nf-core/mag/pull/575/files) - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133) +- [#575](https://github.com/nf-core/mag/pull/575) - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133) ### `Fixed`