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‎.nf-core.yml‎

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lint:
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multiqc_config: false
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files_exist:
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- tests/default.nf.test
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files_unchanged:
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- .github/CONTRIBUTING.md
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- docs/images/nf-core-seqinspector_logo_dark.png
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- docs/images/nf-core-seqinspector_logo_light.png
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- assets/nf-core-seqinspector_logo_light.png
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nextflow_config:
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- config_defaults:
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- params.fastq_screen_references

‎CHANGELOG.md‎

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@@ -26,9 +26,14 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
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- [#86](https://github.com/nf-core/seqinspector/issues/86) Update lists of default steps in the pipeline
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- [#84](https://github.com/nf-core/seqinspector/issues/84) Short summary of seqinspector in README.md
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- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
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- [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
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- [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
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- [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
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- [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
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- [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
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- [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
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- [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
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- [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
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### `Fixed`
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- [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
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- [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
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- [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
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- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
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- [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
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### `Dependencies`
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‎CITATIONS.md‎

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- [Picard Tools](https://broadinstitute.github.io/picard/)
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> Broad Institute, “Picard Toolkit.” 2019. GitHub Repository. https://broadinstitute.github.io/picard/
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## Software packaging/containerisation tools
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- [Anaconda](https://anaconda.com)

‎README.md‎

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<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
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| Tool Type | Tool Name | Tool Description | Compatibility with Data | Dependencies |
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| ------------------- | ---------------------------------------------------------------------------------- | ------------------------------------------- | ----------------------- | ------------------- |
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| `Subsampling` | [`Seqtk`](https://github.com/lh3/seqtk) | Global subsampling of reads | [RNA, DNA, synthetic] | [N/A] |
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| `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] |
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| `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] |
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| `QC` | [`SeqFu Stats`](https://github.com/telatin/seqfu2) | Sequence statistics | [RNA, DNA] | [N/A] |
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| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] |
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| `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] |
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| `QC` | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics | [RNA, DNA] | [Bwamem2, SAMtools] |
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| `Reporting` | [`MultiQC`](http://multiqc.info/) | Aggregate and visualise results | [RNA, DNA, synthetic] | [N/A] |
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| Tool Type | Tool Name | Tool Description | Compatibility with Data | Dependencies | Default tool |
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| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |
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| `Subsampling` | [`Seqtk`](https://github.com/lh3/seqtk) | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic] | [N/A] | no |
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| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] | yes |
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| `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes |
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| `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] | yes |
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| `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] | yes |
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| `QC` | [`SeqFu Stats`](https://github.com/telatin/seqfu2) | Sequence statistics | [RNA, DNA] | [N/A] | yes |
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| `QC` | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics | [RNA, DNA] | [Bwamem2, SAMtools, `--genome`] | yes |
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| `QC` | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data. | [RNA, DNA] | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |
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| `Reporting` | [`MultiQC`](http://multiqc.info/) | Present QC for raw reads | [RNA, DNA, synthetic] | [N/A] | yes |
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<picture>
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<source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">
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## Credits
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nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).
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nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).
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We thank the following people for their extensive assistance in the development of this pipeline:
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## Citations
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<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
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<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
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<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
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An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

‎assets/methods_description_template.yml‎

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section_name: "nf-core/seqinspector Methods Description"
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section_href: "https://github.com/nf-core/seqinspector"
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plot_type: "html"
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## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
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## You inject any metadata in the Nextflow '${workflow}' object
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data: |
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<h4>Methods</h4>
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<p>Data was processed using nf-core/seqinspector v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>

‎assets/multiqc_config.yml‎

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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-seqinspector-index":
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order: -999
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"nf-core-seqinspector-methods-description":
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order: -1000
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software_versions:
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multiqc_software_versions:
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order: -1001
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"nf-core-seqinspector-summary":
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order: -1002

‎assets/nf-core-seqinspector_logo_light.png‎

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‎conf/modules.config‎

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}
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withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
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publishDir = [
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path: { "${params.outdir}/picard_createsequencedictionary" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: 'BWAMEM2_MEM' {
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path: { "${params.outdir}/bwamem2_mem" },
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}
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withName: 'PICARD_COLLECTHSMETRICS' {
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publishDir = [
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path: { "${params.outdir}/picard_collecthsmetrics" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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ext.args = {"--TMP_DIR ."}
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}
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withName: 'SAMTOOLS_FAIDX' {
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publishDir = [
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path: { "${params.outdir}/samtools_faidx" },

‎docs/images/nf-core-seqinspector_logo_dark.png‎

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‎docs/images/nf-core-seqinspector_logo_light.png‎

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