Skip to content

docs: build site with experimental sprocket branch #299

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
a-frantz wants to merge 3 commits into
base: main
Choose a base branch
from
Draft

docs: build site with experimental sprocket branch #299

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
3531c46
hijack the pages site for sprocket staging
a-frantz Feb 18, 2026
bfc7760
use doc comments for structs
a-frantz Feb 18, 2026
4e38f29
add a strandedness enum
a-frantz Feb 23, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions .github/workflows/cd.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ on:
push:
branches:
- main
- staging/sprocket-doc

jobs:
gh-pages:
Expand All @@ -17,11 +18,11 @@ jobs:
run: rustup update stable && rustup default stable
- name: Build Sprocket
run: |
cargo install sprocket --locked
cargo install sprocket --locked --git https://github.com/Serial-ATA/sprocket.git --branch doc-tables
- name: Build Docs
run: |
cd $GITHUB_WORKSPACE/workflows
sprocket dev doc -v --homepage assets/DOCS.md --prioritize-workflows-view .
sprocket dev doc --homepage assets/DOCS.md --with-doc-comments .
cp -r assets docs/
- name: Deploy
uses: peaceiris/actions-gh-pages@v4
Expand Down
20 changes: 11 additions & 9 deletions data_structures/flag_filter.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
## # FlagFilter
##
version 1.1

## A struct to represent the filtering flags used in various `samtools` commands.
##
## The order of precedence is `include_if_all`, `exclude_if_any`, `include_if_any`,
## and `exclude_if_all`.
## These four fields correspond to the samtools flags
Expand Down Expand Up @@ -58,14 +59,15 @@
## In short, those are all flags corresponding to the quality of the read
## and them being `true` may indicate that the read is of low quality and
## should be excluded.

version 1.1

struct FlagFilter {
String include_if_all # samtools -f
String exclude_if_any # samtools -F
String include_if_any # samtools --rf
String exclude_if_all # samtools -G
## Corresponds to `samtools -f`
String include_if_all
## Corresponds to `samtools -F`
String exclude_if_any
## Corresponds to `samtools --rf`
String include_if_any
## Corresponds to `samtools -G`
String exclude_if_all
}

task validate_string_is_12bit_int {
Expand Down
66 changes: 33 additions & 33 deletions data_structures/read_group.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,32 +1,7 @@
## Read groups are defined in the SAM spec
## - `ID`: Read group identifier. Each Read Group must have a unique ID.
## The value of ID is used in the RG tags of alignment records.
## - `BC`: Barcode sequence identifying the sample or library. This value is the
## expected barcode bases as read by the sequencing machine in the absence
## of errors. If there are several barcodes for the sample/library
## (e.g., one on each end of the template), the recommended implementation
## concatenates all the barcodes separating them with hyphens (`-`).
## - `CN`: Name of sequencing center producing the read.
## - `DS`: Description.
## - `DT`: Date the run was produced (ISO8601 date or date/time).
## - `FO`: Flow order. The array of nucleotide bases that correspond to the nucleotides
## used for each flow of each read. Multi-base flows are encoded in IUPAC format,
## and non-nucleotide flows by various other characters.
## Format: `/\\*|[ACMGRSVTWYHKDBN]+/`
## - `KS`: The array of nucleotide bases that correspond to the key sequence of each read.
## - `LB`: Library.
## - `PG`: Programs used for processing the read group.
## - `PI`: Predicted median insert size, rounded to the nearest integer.
## - `PL`: Platform/technology used to produce the reads.
## Valid values: CAPILLARY, DNBSEQ (MGI/BGI), ELEMENT, HELICOS, ILLUMINA, IONTORRENT,
## LS454, ONT (Oxford Nanopore), PACBIO (Pacific Biosciences), SINGULAR, SOLID,
## and ULTIMA. This field should be omitted when the technology is not in this list
## (though the PM field may still be present in this case) or is unknown.
## - `PM`: Platform model. Free-form text providing further details of the
## platform/technology used.
## - `PU`: Platform unit (e.g., flowcell-barcode.lane for Illumina or slide
## for SOLiD). Unique identifier.
## - `SM`: Sample. Use pool name where a pool is being sequenced.
version 1.1

## Read groups are defined in the SAM specification. This struct
## provides utlity for constructing, validating, and parsing read groups.
##
## An example input JSON entry for `read_group` might look like this:
## ```json
Expand All @@ -40,25 +15,50 @@
## }
## }
## ```

version 1.1

#@ except: SnakeCase
struct ReadGroup {
## `ID`: Read group identifier. Each Read Group must have a unique ID.
## The value of ID is used in the RG tags of alignment records.
String ID
String? BC
## `CN`: Name of sequencing center producing the read.
String? CN
## `DS`: Description.
String? DS
## `DT`: Date the run was produced (ISO8601 date or date/time).
String? DT
## `FO`: Flow order. The array of nucleotide bases that correspond to the nucleotides
## used for each flow of each read. Multi-base flows are encoded in IUPAC format,
## and non-nucleotide flows by various other characters.
## Format: `/\\*|[ACMGRSVTWYHKDBN]+/`
String? FO
## `KS`: The array of nucleotide bases that correspond to the key sequence of each read.
String? KS
## `LB`: Library.
String? LB
## `PG`: Programs used for processing the read group.
String? PG
## `PI`: Predicted median insert size, rounded to the nearest integer.
Int? PI
## `PL`: Platform/technology used to produce the reads.
## Valid values: CAPILLARY, DNBSEQ (MGI/BGI), ELEMENT, HELICOS, ILLUMINA, IONTORRENT,
## LS454, ONT (Oxford Nanopore), PACBIO (Pacific Biosciences), SINGULAR, SOLID,
## and ULTIMA. This field should be omitted when the technology is not in this list
## (though the PM field may still be present in this case) or is unknown.
String? PL
## `PM`: Platform model. Free-form text providing further details of the
## platform/technology used.
String? PM
## `PU`: Platform unit (e.g., flowcell-barcode.lane for Illumina or slide
## for SOLiD). Unique identifier.
String? PU
## `SM`: Sample. Use pool name where a pool is being sequenced.
String? SM
## `BC`: Barcode sequence identifying the sample or library. This value is the
## expected barcode bases as read by the sequencing machine in the absence
## of errors. If there are several barcodes for the sample/library
## (e.g., one on each end of the template), the recommended implementation
## concatenates all the barcodes separating them with hyphens (`-`).
String? BC
}

workflow read_group_to_string {
Expand Down
16 changes: 16 additions & 0 deletions data_structures/strandedness.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
version 1.3

## Possible strandedness protocols used during RNA-Seq library prep.
enum Strandedness {
## The protocol is unknown or otherwise unspecified.
##
## Some tooling can automatically derive a suspected strandedness protocol,
## if one is not specified.
Unspecified,
## The RNA-Seq library was prepped with an unstranded protocol.
Unstranded,
## The RNA-Seq library was prepped with a Stranded-Reverse protocol.
StrandedReverse,
## The RNA-Seq library was prepped with a Stranded-Forward protocol.
StrandedForward,
}
Loading