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docs: regenerate nf-fgsv example for fg-labs org move #11

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338 changes: 127 additions & 211 deletions docs/examples/nf-fgsv/index.html
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128 changes: 62 additions & 66 deletions docs/examples/nf-fgsv/json/pipeline-api.json
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4 changes: 2 additions & 2 deletions docs/examples/nf-fgsv/markdown/index.md
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Expand Up @@ -22,9 +22,9 @@ Nextflow workflow for running fgsv.

## Links

- [Repository](https://github.com/fulcrumgenomics/nf-fgsv)
- [Repository](https://github.com/fg-labs/nf-fgsv)

---

*This pipeline was built with [Nextflow](https://nextflow.io).
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
9 changes: 7 additions & 2 deletions docs/examples/nf-fgsv/markdown/inputs.md
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Expand Up @@ -8,7 +8,12 @@ This page documents all input parameters for the pipeline.

**Type:** `string` | **Required** | **Format:** `file-path`

Path to tab-separated file containing information about the samples in the experiment.
Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns:

- `sample`: a unique sample identifier containing no whitespace; used as the `meta.id` that names per-sample outputs.
- `bam`: path to an existing BAM file for the sample (must end in `.bam`).

See `schemas/input_schema.json` for the full validation rules.

**Pattern:** `.*.tsv$`

Expand All @@ -17,4 +22,4 @@ Path to tab-separated file containing information about the samples in the exper
---

*This pipeline was built with [Nextflow](https://nextflow.io).
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
42 changes: 11 additions & 31 deletions docs/examples/nf-fgsv/markdown/processes.md
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Expand Up @@ -20,13 +20,8 @@ AggregateSvPileupToBedPE.

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file |

### Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_svpileup.aggregate.bedpe")` | `tuple` | `bedpe` | Tuple of meta and BEDPE format output file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `txt` | `path` | Aggregated SvPileup output file |


## AGGREGATE_SV_PILEUP {#aggregate-sv-pileup}
Expand All @@ -40,13 +35,9 @@ using fgsv AggregateSvPileup.

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(bam), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file |

### Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_svpileup.aggregate.txt")` | `tuple` | `txt` | Tuple of meta and aggregated SvPileup output file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `bam` | `path` | Input BAM file |
| `txt` | `path` | SvPileup breakpoint output file |


## COORDINATE_SORT {#coordinate-sort}
Expand All @@ -59,36 +50,25 @@ Sort a BAM file by genomic coordinates using samtools sort.

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted |

### Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_sorted.bam")` | `tuple` | `bam` | Tuple of meta and coordinate-sorted BAM file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `bam` | `path` | Input BAM file to be sorted |


## SV_PILEUP {#sv-pileup}

*Defined in `modules/sv_pileup.nf:11`*
*Defined in `modules/sv_pileup.nf:10`*

Detect structural variant evidence from a BAM file using fgsv SvPileup.

### Inputs

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file |

### Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_svpileup.txt")` | `tuple` | `txt` | Tuple of meta and SvPileup breakpoint output file |
| `val(meta), file("*_svpileup.bam")` | `tuple` | `bam` | Tuple of meta and SvPileup BAM file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `bam` | `path` | Input BAM file |


---

*This pipeline was built with [Nextflow](https://nextflow.io).
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
15 changes: 13 additions & 2 deletions docs/examples/nf-fgsv/markdown/workflows.md
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Expand Up @@ -10,10 +10,21 @@ This page documents all workflows in the pipeline.

**Entry workflow**

*Defined in `main.nf:19`*
*Defined in `main.nf:35`*

Detect structural-variant breakpoints from aligned reads using fgsv.
The `--input` sample sheet provides one `sample` identifier and `bam` path per
row (see the `--input` parameter for the full column specification). Every
per-sample output — the sorted BAM, SvPileup BAM and text, aggregated
breakpoints, and BEDPE — is published via the `sample_outputs` topic into a
directory named after the sample's `meta.id`. For each sample the workflow runs:
1. `COORDINATE_SORT` — coordinate-sort the input BAM with samtools.
2. `SV_PILEUP` — gather read-level evidence for structural variants (fgsv SvPileup).
3. `AGGREGATE_SV_PILEUP` — merge pileups that likely support the same breakpoint.
4. `AGGREGATE_SV_PILEUP_TO_BEDPE` — convert the aggregated breakpoints to BEDPE.


---

*This pipeline was built with [Nextflow](https://nextflow.io).
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:33 UTC.*
44 changes: 12 additions & 32 deletions docs/examples/nf-fgsv/table/README.md
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Expand Up @@ -9,13 +9,13 @@

| Name | Description | Type | Default | Required |
|------|-------------|------|---------|:--------:|
| `--input` | Path to tab-separated file containing information about the samples in the experiment. | `string` | n/a | yes |
| `--input` | Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns: - `sample`: a unique sample identifier containing no whitespace; used as the `meta.id` that names per-sample outputs. - `bam`: path to an existing BAM file for the sample (must end in `.bam`). See `schemas/input_schema.json` for the full validation rules. | `string` | n/a | yes |

## Workflows

| Name | Description | Entry |
|------|-------------|:-----:|
| *(entry)* | n/a | yes |
| *(entry)* | Detect structural-variant breakpoints from aligned reads using fgsv. The `--input` sample sheet provides one `sample` identifier and `bam` path per row (see the `--input` parameter for the full column specification). Every per-sample output — the sorted BAM, SvPileup BAM and text, aggregated breakpoints, and BEDPE — is published via the `sample_outputs` topic into a directory named after the sample's `meta.id`. For each sample the workflow runs: 1. `COORDINATE_SORT` — coordinate-sort the input BAM with samtools. 2. `SV_PILEUP` — gather read-level evidence for structural variants (fgsv SvPileup). 3. `AGGREGATE_SV_PILEUP` — merge pileups that likely support the same breakpoint. 4. `AGGREGATE_SV_PILEUP_TO_BEDPE` — convert the aggregated breakpoints to BEDPE. | yes |

## Processes

Expand All @@ -30,54 +30,34 @@

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file |

### `AGGREGATE_SV_PILEUP_TO_BEDPE` Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_svpileup.aggregate.bedpe")` | `tuple` | `bedpe` | Tuple of meta and BEDPE format output file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `txt` | `path` | Aggregated SvPileup output file |

### `AGGREGATE_SV_PILEUP` Inputs

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(bam), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file |

### `AGGREGATE_SV_PILEUP` Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_svpileup.aggregate.txt")` | `tuple` | `txt` | Tuple of meta and aggregated SvPileup output file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `bam` | `path` | Input BAM file |
| `txt` | `path` | SvPileup breakpoint output file |

### `COORDINATE_SORT` Inputs

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted |

### `COORDINATE_SORT` Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_sorted.bam")` | `tuple` | `bam` | Tuple of meta and coordinate-sorted BAM file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `bam` | `path` | Input BAM file to be sorted |

### `SV_PILEUP` Inputs

| Name | Type | Description |
|------|------|-------------|
| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file |

### `SV_PILEUP` Outputs

| Name | Type | Emit | Description |
|------|------|------|-------------|
| `val(meta), file("*_svpileup.txt")` | `tuple` | `txt` | Tuple of meta and SvPileup breakpoint output file |
| `val(meta), file("*_svpileup.bam")` | `tuple` | `bam` | Tuple of meta and SvPileup BAM file |
| `meta` | `val` | Map containing sample information (must include 'id') |
| `bam` | `path` | Input BAM file |

---

*This pipeline was built with [Nextflow](https://nextflow.io).
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 22:49:08 UTC.*
Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.3.0 on 2026-05-27 21:22:48 UTC.*

<!-- END_NF_DOCS -->
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