nf-core/chipseq: nf-core/chipseq v2.1.0 - Platinum Willow Sparrow

[2.1.0] - 2024-10-07

Enhancements & fixes

• Updated pipeline template to nf-core/tools 2.7.2
• [#317] - Added metro map
• [#288] - Bump chromap version 2 and enable all the steps below chromap again when paired-end data is processed.
• [#311] - Add back --skip_spp parameter which was unintentionally removed from the code.
• Install available nf-core subworkflows and refactor code accordingly
• [#318] - Update bowtie2/align module to fix issue when downloading its singularity image.
• [#320] - Fix samplesheet control column in documentation examples.
• [#328] - Modify documentation to clarify that is necessary to provide the --read_length when --genome is set and --macs_gsize has not provided.
• Remove enable_conda param from local modules.
• Fix the path where chromap index is stored when --save_reference is set.
• Fix untar of chromap index when using --chromap_index param.
• nf-core/tools#2286 - Set default container registry outside profile scope.
• [#343] - Provide replicate information explicitly in samplesheet.
• Updated pipeline template to nf-core/tools 2.10.
• [#367] - Get rid of CheckIfExists for params paths.
• [#370] - Fix stack overflow exceptions in phantompeakqualtools (see here).
• [#387] - Get rid of the lib folder and rearrange the pipeline accordingly.
• [#385] - Fix --save_unaligned description in schema.
• [PR #392] - Adding line numbers to warnings/errors messages in bin/check_samplesheet.py.
• [#396] - Check that samplesheet samples IDs do only have alphanumeric characters, dots, dashes or underscores.
• [#378] - Switch from macs2 to macs3.
• [#347] - Add read group tag to bam files processed by bowtie2.
• [PR #406] - Update metro map to show macs3 instead of macs2.
• [#409] - Bulk modules and subworkflows update.
• [PR #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. 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.

| Dependency | Old version | New version | | ----------------------- | ----------- | ----------- | | bowtie2 | 2.4.4 | 2.5.2 | | bwa | 0.7.17 | 0.7.18 | | chromap | 0.2.1 | 0.2.6 | | deeptools | 3.5.1 | 3.5.5 | | fastqc | 0.11.9 | 0.12.1 | | 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 | | ucsc-bedgraphtobigwig | 377 | 445 | | umi_tools | | 1.1.5 |

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.