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maxulysse merged 7 commits into from
Feb 23, 2026
Merged

Fix schema and docs #178

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e3567b0
Fix schema and docs
maxulysse Feb 23, 2026
762cfa4
better icons
maxulysse Feb 23, 2026
95c03b9
Apply suggestion from @maxulysse
maxulysse Feb 23, 2026
1847c29
better icons
maxulysse Feb 23, 2026
120e25b
no need to hide these params
maxulysse Feb 23, 2026
e7ab28a
Update nextflow_schema.json
maxulysse Feb 23, 2026
2359a1f
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maxulysse Feb 23, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#173](https://github.com/nf-core/seqinspector/pull/173) Fix warning message for tag name collision
- [#174](https://github.com/nf-core/seqinspector/pull/174) Fix null message when no rundir information is available
- [#175](https://github.com/nf-core/seqinspector/pull/175) Fix conda setup in CI
- [#178](https://github.com/nf-core/seqinspector/pull/178) Fix nextflow schema
- [#178](https://github.com/nf-core/seqinspector/pull/178) Fix links in documentation

### `Changed`

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4 changes: 2 additions & 2 deletions docs/output.md
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Expand Up @@ -12,8 +12,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat

- [Seqtk](#seqtk) - Subsample a specific number of reads per sample
- [FastQC](#fastqc) - Raw read QC
- [SeqFu Stats](#seqfu_stats) - Statistics for FASTA or FASTQ files
- [FastQ Screen](#fastqscreen) - Mapping against a set of references for basic contamination QC
- [SeqFu Stats](#seqfu-stats) - Statistics for FASTA or FASTQ files
- [FastQ Screen](#fastq-screen) - Mapping against a set of references for basic contamination QC
- [BWA-MEM2_INDEX](#bwamem2_index) - Create BWA-MEM2 index of a chosen reference genome OR use pre-built index
- [BWA-MEM2_MEM](#bwamem2_mem) - Mapping reads against a chosen reference genome
- [Samtools index](#samtools-index) - Index BAM files with Samtools
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99 changes: 48 additions & 51 deletions nextflow_schema.json
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Expand Up @@ -27,7 +27,8 @@
"type": "number",
"description": "Take a subset of reads for analysis.",
"help_text": "Subset can be used as a fraction of reads (ex/ 0.20) or an absolute number of reads per sample (integer). Pipeline will still run if a sample has less reads than selected subset value.",
"default": 0
"default": 0,
"fa_icon": "fas fa-arrows-alt-h"
},
"outdir": {
"type": "string",
Expand All @@ -47,10 +48,24 @@
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
},
"run_picard_collecthsmetrics": {
"type": "boolean",
"hidden": true,
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@maxulysse maxulysse Feb 23, 2026

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Suggested change
"hidden": true,

"description": "Run picard_collecthsmetrics for QC of bam files.",
"fa_icon": "fas fa-play"
},
"skip_tools": {
"type": "string",
"description": "Comma-separated string of tools to skip",
"pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index|rundirparser)?,?)*(?<!,)$"
"pattern": "^((bwamem2_index|bwamem2_mem|fastqc|fastqscreen|picard_collectmultiplemetrics|rundirparser|samtools_faidx|samtools_index|seqfu_stats|seqtk_sample)?,?)*(?<!,)$",
"fa_icon": "fas fa-fast-forward"
},
"sort_bam": {
"type": "boolean",
"default": true,
"description": "Sort BAM files after alignment",
"help_text": "If true, BAM files produced by alignment will be sorted by genomic coordinates.",
"fa_icon": "fas fa-sort-alpha-down"
}
}
},
Expand All @@ -73,7 +88,7 @@
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically.",
"fa_icon": "far fa-file-code"
},
"igenomes_ignore": {
Expand Down Expand Up @@ -101,18 +116,34 @@
"type": "string",
"format": "directory-path",
"exists": true,
"fa_icon": "fas fa-copy",
"description": "Path to BWA mem indices.",
"fa_icon": "fas fa-folder-open",
"description": "Path to bwamem2 indices.",
"help_text": "If you wish to recompute indices available on igenomes, set `--bwamem2 false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference.\n\nIf you use AWS iGenomes, this has already been set for you appropriately."
},
"dict": {
"type": "string",
"hidden": true,
"description": "Sequence dictionary for the reference fasta file provided.",
"help_text": "If you wish to recompute indices available on igenomes, set `--ic false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference.\n\nIf you use AWS iGenomes, this has already been set for you appropriately.",
"pattern": "^\\S+.dict$",
"format": "file-path",
"exists": true
"exists": true,
"fa_icon": "fas fa-file"
},
"target_intervals": {
"type": "string",
"description": "Path to target intervals file.",
"pattern": "^\\S+.(bed|bed.gz|interval_list)$",
"format": "file-path",
"exists": true,
"fa_icon": "fas fa-file"
},
"bait_intervals": {
"type": "string",
"description": "Path to bait intervals file.",
"pattern": "^\\S+.(bed|bed.gz|interval_list)$",
"format": "file-path",
"exists": true,
"fa_icon": "fas fa-file"
}
}
},
Expand Down Expand Up @@ -177,12 +208,6 @@
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"sort_bam": {
"type": "boolean",
"default": true,
"description": "Sort BAM files after alignment",
"help_text": "If true, BAM files produced by alignment will be sorted by genomic coordinates."
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
Expand Down Expand Up @@ -223,15 +248,16 @@
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"fa_icon": "fas fa-link",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"modules_testdata_base_path": {
"type": "string",
"description": "Base path / URL for data used in the modules",
"hidden": true,
"default": "s3://ngi-igenomes/testdata/nf-core/modules/"
"default": "s3://ngi-igenomes/testdata/nf-core/modules/",
"fa_icon": "fas fa-map"
},
"multiqc_config": {
"type": "string",
Expand Down Expand Up @@ -267,50 +293,24 @@
},
"trace_report_suffix": {
"type": "string",
"fa_icon": "far calendar",
"fa_icon": "fas fa-tag",
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
},
"help": {
"type": ["boolean", "string"],
"description": "Display the help message."
"description": "Display the help message.",
"fa_icon": "fas fa-info"
},
"help_full": {
"type": "boolean",
"description": "Display the full detailed help message."
"description": "Display the full detailed help message.",
"fa_icon": "fas fa-question-circle"
},
"show_hidden": {
"type": "boolean",
"description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
}
}
},
"picard_collecthsmetrics_options": {
"title": "picard_collecthsmetrics options",
"type": "object",
"description": "",
"default": "",
"properties": {
"run_picard_collecthsmetrics": {
"type": "boolean",
"hidden": true,
"description": "Run picard_colecthsmetrics for QC of bam files."
},
"bait_intervals": {
"type": "string",
"description": "Path to bait intervals file.",
"hidden": true,
"pattern": "^\\S+.(bed|bed.gz|interval_list)$",
"format": "file-path",
"exists": true
},
"target_intervals": {
"type": "string",
"description": "Path to target intervals file.",
"hidden": true,
"pattern": "^\\S+.(bed|bed.gz|interval_list)$",
"format": "file-path",
"exists": true
"description": "Display hidden parameters in the help message (only works when --help or --help_full are provided).",
"fa_icon": "fas fa-eye"
}
}
}
Expand All @@ -327,9 +327,6 @@
},
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/picard_collecthsmetrics_options"
}
]
}
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