Merge pull request #418 from JoseEspinosa/updates

Apply review suggestions

Author: JoseEspinosa

CHANGELOG.md

@@ -3,7 +3,23 @@
 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
+
+### Credits
+
+Special thanks to the following people for their contributions to this 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
 
@@ -33,6 +49,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#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.
@@ -45,13 +75,11 @@ 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       |
 

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).
 

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

docs/output.md

@@ -80,6 +80,7 @@ The `--save_unaligned` parameter enables to obtain FastQ files containing unmapp
 
 <details markdown="1">
     <summary>Output files</summary>
+
 - `<ALIGNER>/library/unmapped/`
   - `*.fastq.gz`: If `--save_unaligned` is specified, FastQ files containing unmapped reads will be placed in this directory.
 

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.
 

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

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",

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