From 0f18b6265583227de56c8eccc49b08eef7fa9554 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 16:15:21 +0200 Subject: [PATCH 01/12] Apply review sugestions on schema --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 7189751b..20e71c94 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -91,7 +91,7 @@ "pattern": "^\\S+\\.gtf(\\.gz)?$", "description": "Path to GTF annotation file.", "fa_icon": "fas fa-code-branch", - "help_text": "This parameter is *mandatory* if `--genome` is not specified." + "help_text": "Either this parameter or `--gff` is *mandatory* if --genome is not specified." }, "gff": { "type": "string", @@ -101,7 +101,7 @@ "pattern": "^\\S+\\.gff(\\.gz)?$", "fa_icon": "fas fa-code-branch", "description": "Path to GFF3 annotation file.", - "help_text": "This parameter must be specified if `--genome` or `--gtf` are not specified." + "help_text": "Either this parameter or `--gtf` is *mandatory* if --genome is not specified." }, "bwa_index": { "type": "string", From e5c1a9790a14793c70e25a628c693da7ae190a81 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 16:17:22 +0200 Subject: [PATCH 02/12] Removed duplicated lines --- CHANGELOG.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d0c3b83c..be24ed81 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,13 +45,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | `deeptools` | 3.5.1 | 3.5.5 | | `fastqc` | 0.11.9 | 0.12.1 | | `gffread` | 0.12.1 | 0.12.7 | -| `gffread` | 0.12.1 | 0.12.7 | | `macs2` | 2.2.7.1 | | | `macs3` | | 3.0.1 | | `multiqc` | 1.13 | 1.23 | | `picard` | 2.27.4 | 3.2.0 | | `samtools` | 1.15.1 | 1.20 | -| `samtools` | 1.15.1 | 1.20 | | `ucsc-bedgraphtobigwig` | 377 | 445 | | `umi_tools` | | 1.1.5 | From bfcd696b51d111b69328806d7b2c0e13c3cae428 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 16:17:32 +0200 Subject: [PATCH 03/12] Fix tyop --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e6160daf..f1347da5 100644 --- a/README.md +++ b/README.md @@ -110,7 +110,7 @@ For more details about the output files and reports, please refer to the These scripts were originally written by Chuan Wang ([@chuan-wang](https://github.com/chuan-wang)) and Phil Ewels ([@ewels](https://github.com/ewels)) for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. The pipeline was re-implemented by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and converted to Nextflow DSL2 by Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/). -The pipeline workflow diagram was designe by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)). +The pipeline workflow diagram was designed by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)). Many thanks to others who have helped out and contributed along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@bc2zb](https://github.com/bc2zb), [@bjlang](https://github.com/bjlang), [@crickbabs](https://github.com/crickbabs), [@drejom](https://github.com/drejom), [@houghtos](https://github.com/houghtos), [@KevinMenden](https://github.com/KevinMenden), [@mashehu](https://github.com/mashehu), [@pditommaso](https://github.com/pditommaso), [@Rotholandus](https://github.com/Rotholandus), [@sofiahaglund](https://github.com/sofiahaglund), [@tiagochst](https://github.com/tiagochst) and [@winni2k](https://github.com/winni2k). From 15a91e5e3a881998bd73072a41a31cca60aac301 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 16:17:59 +0200 Subject: [PATCH 04/12] Include DOI in nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 425fa2f8..2f01313f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -292,7 +292,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '2.1.0' - doi = '' + doi = 'https://doi.org/10.5281/zenodo.3240506' } // Load modules.config for DSL2 module specific options From a08fda9436cc8ace725c3468c4e1d04e2a4736b4 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 16:18:23 +0200 Subject: [PATCH 05/12] Correct index for printing error --- bin/check_samplesheet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index c7d8add7..d34f42ed 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -222,7 +222,7 @@ def check_samplesheet(file_in, file_out): print_error( f"Control identifier and replicate has to match a provided sample identifier and replicate!", "Control", - val[4], + val[-1], ) ## Write to file From fcaeea44b783597703c08b29efbcda72ebda3057 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 16:18:44 +0200 Subject: [PATCH 06/12] Apply review suggestion --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index cce83421..31a0966f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -14,7 +14,7 @@ You will need to create a samplesheet with information about the samples you wou ### Multiple replicates -The `sample` identifier should be identical when you have multiple replicates from the same experimental group, just increment the `replicate` identifier appropriately. The first replicate value for any given experimental group must be 1. +The `sample` identifier should be identical when you have multiple replicates from the same experimental group; just increment the `replicate` identifier appropriately. The first replicate value for any given experimental group must be 1. The `antibody` column is required to separate the downstream consensus peak merging for different antibodies. It is not advisable to generate a consensus peak set across different antibodies especially if their binding patterns are inherently different e.g. narrow transcription factors and broad histone marks. @@ -184,7 +184,7 @@ nextflow pull nf-core/chipseq It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest pipeline version - numeric only (eg. `2.0.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.0.0`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chipseq/releases) and find the latest pipeline version - numeric only (eg. `2.1.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.1.0`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. From b626b671559ab502c8e97bc5dce5ae6c5ac28331 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 16:18:58 +0200 Subject: [PATCH 07/12] Remove todo --- workflows/chipseq.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf index 32b44a9d..a0013cc8 100644 --- a/workflows/chipseq.nf +++ b/workflows/chipseq.nf @@ -425,7 +425,6 @@ workflow CHIPSEQ { // // MODULE: Calculute genome size with khmer // - // TODO move to prepare genome ch_macs_gsize = Channel.empty() ch_subreadfeaturecounts_multiqc = Channel.empty() ch_macs_gsize = params.macs_gsize From 6998300feeff5a0137783a7cb92dd733696817f2 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 1 Oct 2024 22:15:22 +0200 Subject: [PATCH 08/12] Add release date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index be24ed81..58a47f0f 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). -## v2.1.0 - [date] +## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-02 ### Enhancements & fixes From 224ea8c66e69681f1ea5260ef157b8e0c5934fd8 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 2 Oct 2024 09:49:39 +0200 Subject: [PATCH 09/12] Add release credits --- CHANGELOG.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 58a47f0f..8c993a24 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-02 +### Credits + +Special thanks to the following for their contributions to the release: + +- [Adam Talbot](https://github.com/adamrtalbot) +- [Björn Langer](https://github.com/bjlang) +- [Konrad Rokicki](https://github.com/krokicki) +- [Matthias Hörtenhuber](https://github.com/mashehu) +- [Maxime Garcia](https://github.com/maxulysse) +- [Samuel Ruiz Pérez](https://github.com/samuelruizperez) +- [Sarah Guinchard](https://github.com/g-sarah) +- [Sateesh Peri](https://github.com/sateeshperi) +- [Steffen Möller](https://github.com/smoe) + +Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. + ### Enhancements & fixes - Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2) From 44a596c3572526ee0d78960a4b41d97699a41072 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 2 Oct 2024 10:47:09 +0200 Subject: [PATCH 10/12] Add parameters to changelog --- CHANGELOG.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c993a24..3e061f46 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -49,6 +49,20 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [[#409](https://github.com/nf-core/chipseq/issues/409)] - Bulk modules and subworkflows update. - [[PR #415](https://github.com/nf-core/chipseq/pull/415)] - Get rid of `oras` in modules. +### Parameters + +| Old parameter | New parameter | +| ---------------------- | ------------------------------------ | +| `--show_hidden_params` | `--validationShowHiddenParams` | +| | `--version` | +| | `--hook_url` | +| | `--multiqc_logo` | +| | `--multiqc_methods_description` | +| | `--pipelines_testdata_base_path` | +| | `--validationFailUnrecognisedParams` | +| | `--validationLenientMode` | +| `--enable_conda` | | + ### Software dependencies Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. From 683728ad7b358c9898f8c158470f8616f5b82269 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 2 Oct 2024 11:39:11 +0200 Subject: [PATCH 11/12] Correct credits text --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e061f46..cdde3c09 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 ### Credits -Special thanks to the following for their contributions to the release: +Special thanks to the following people for their contributions to this release: - [Adam Talbot](https://github.com/adamrtalbot) - [Björn Langer](https://github.com/bjlang) From b880175c62f5fd40bbe058edd98f18f86969499b Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 2 Oct 2024 16:07:28 +0200 Subject: [PATCH 12/12] Fix output files rendering error (missing line) --- docs/output.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/output.md b/docs/output.md index 2cee73ef..a1336953 100644 --- a/docs/output.md +++ b/docs/output.md @@ -80,6 +80,7 @@ The `--save_unaligned` parameter enables to obtain FastQ files containing unmapp
Output files + - `/library/unmapped/` - `*.fastq.gz`: If `--save_unaligned` is specified, FastQ files containing unmapped reads will be placed in this directory.