Skip to content

Commit

Permalink
updates, rm req column in favor of badges
Browse files Browse the repository at this point in the history
  • Loading branch information
@pdimens
pdimens committed Nov 8, 2024
1 parent f932bf2 commit 25a4c4d
Show file tree
Hide file tree
Showing 22 changed files with 319 additions and 176 deletions.
18 changes: 9 additions & 9 deletions Workflows/Align/bwa.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,15 +32,15 @@ harpy align bwa --genome genome.fasta Sequences/
In addition to the [!badge variant="info" corners="pill" text="common runtime options"](/commonoptions.md), the [!badge corners="pill" text="align bwa"] module is configured using these command-line arguments:

{.compact}
| argument | short name | type | default | required | description |
|:-------------------|:----------:|:----------------------|:-------:|:--------:|:------------------------------------------------------|
| `INPUTS` | | file/directory paths | | ‼️ | Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments) |
| `--contigs` | | file path or list | | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | string | | | Additional EMA-align/BWA arguments, in quotes |
| `--genome` | `-g` | file path | | ‼️ | Genome assembly for read mapping |
| `--keep-unmapped` | `-u` | toggle | false | | Output unmapped sequences too |
| `--min-quality` | `-q` | integer (0-40) | 30 | | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--molecule-distance` | `-d` | integer | 100000 | | Base-pair distance threshold to separate molecules |
| argument | short name | type | default | description |
| :-------------------- | :--------: | :------------------- | :-----: | :----------------------------------------------------------------------------------------------------------------------------- |
| `INPUTS` | | file/directory paths | | [!badge variant="info" text="required"] Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments) |
| `--contigs` | | file path or list | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | string | | Additional EMA-align/BWA arguments, in quotes |
| `--genome` | `-g` | file path | | [!badge variant="info" text="required"] Genome assembly for read mapping |
| `--keep-unmapped` | `-u` | toggle | false | Output unmapped sequences too |
| `--min-quality` | `-q` | integer (0-40) | 30 | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--molecule-distance` | `-d` | integer | 100000 | Base-pair distance threshold to separate molecules |

### Molecule distance
The `--molecule-distance` option is used during the BWA alignment workflow
Expand Down
24 changes: 12 additions & 12 deletions Workflows/Align/ema.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,18 +41,18 @@ harpy align ema --genome genome.fasta Sequences/
In addition to the [!badge variant="info" corners="pill" text="common runtime options"](/commonoptions.md), the [!badge corners="pill" text="align ema"] module is configured using these command-line arguments:

{.compact}
| argument | short name | type | default | required | description |
|:-------------------|:----------:|:----------------------|:-------:|:--------:|:-------------------------------------------------------------------|
| `INPUTS` | | file/directory paths | | ‼️ | Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments) |
| `--contigs` | | file path or list | | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--fragment-density` | `-d` | toggle | false | | Perform read fragment density optimization |
| `--ema-bins` | `-e` | integer (1-1000) | 500 | | Number of barcode bins for EMA |
| `--extra-params` | `-x` | string | | | Additional EMA-align arguments, in quotes |
| `--genome` | `-g` | file path | | ‼️ | Genome assembly for read mapping |
| `--keep-unmapped` | `-u` | toggle | false | | Output unmapped sequences too |
| `--min-quality` | `-q` | integer (0-40) | 30 | | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--platform` | `-p` | string | haplotag | ‼️ | Linked read technology: `haplotag` or `10x` |
| `--whitelist` | `-w` | file path | | | Path to barcode whitelist (`--platform 10x` only) |
| argument | short name | type | default | description |
| :------------------- | :--------: | :------------------- | :------: | :----------------------------------------------------------------------------------------------------------------------------- |
| `INPUTS` | | file/directory paths | | [!badge variant="info" text="required"] Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments) |
| `--contigs` | | file path or list | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--fragment-density` | `-d` | toggle | false | Perform read fragment density optimization |
| `--ema-bins` | `-e` | integer (1-1000) | 500 | Number of barcode bins for EMA |
| `--extra-params` | `-x` | string | | Additional EMA-align arguments, in quotes |
| `--genome` | `-g` | file path | | [!badge variant="info" text="required"] Genome assembly for read mapping |
| `--keep-unmapped` | `-u` | toggle | false | Output unmapped sequences too |
| `--min-quality` | `-q` | integer (0-40) | 30 | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--platform` | `-p` | string | haplotag | [!badge variant="info" text="required"] Linked read technology: `haplotag` or `10x` |
| `--whitelist` | `-w` | file path | | Path to barcode whitelist (`--platform 10x` only) |

### Barcode whitelist
Some linked-read methods (e.g. 10x, Tellseq) require the inclusion of a barcode "whitelist." This file is a
Expand Down
20 changes: 10 additions & 10 deletions Workflows/Align/strobe.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,16 +32,16 @@ harpy align strobe --genome genome.fasta Sequences/
In addition to the [!badge variant="info" corners="pill" text="common runtime options"](/commonoptions.md), the [!badge corners="pill" text="align strobe"] module is configured using these command-line arguments:

{.compact}
| argument | short name | type | default | required | description |
|:-------------------|:----------:|:----------------------|:-------:|:--------:|:------------------------------------------------------|
| `INPUTS` | | file/directory paths | | ‼️ | Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments) |
| `--contigs` | | file path or list | | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | string | | | Additional EMA-align/BWA arguments, in quotes |
| `--genome` | `-g` | file path | | ‼️ | Genome assembly for read mapping |
| `--keep-unmapped` | `-u` | toggle | false | | Output unmapped sequences too |
| `--min-quality` | `-d` | integer (0-40) | 30 | | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--molecule-distance` | `-m` | integer | 100000 | | Base-pair distance threshold to separate molecules |
| `--read-length` | `-l` | choice | `auto` | | Average read length for creating index. Options: [auto, 50, 75, 100, 125, 150, 250, 400] |
| argument | short name | type | default | description |
| :-------------------- | :--------: | :------------------- | :-----: | :----------------------------------------------------------------------------------------------------------------------------- |
| `INPUTS` | | file/directory paths | | [!badge variant="info" text="required"] Files or directories containing [input FASTQ files](/commonoptions.md#input-arguments) |
| `--contigs` | | file path or list | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | string | | Additional EMA-align/BWA arguments, in quotes |
| `--genome` | `-g` | file path | | [!badge variant="info" text="required"] Genome assembly for read mapping |
| `--keep-unmapped` | `-u` | toggle | false | Output unmapped sequences too |
| `--min-quality` | `-d` | integer (0-40) | 30 | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--molecule-distance` | `-m` | integer | 100000 | Base-pair distance threshold to separate molecules |
| `--read-length` | `-l` | choice | `auto` | Average read length for creating index. Options: [auto, 50, 75, 100, 125, 150, 250, 400] |

### Read Length
The strobealign program uses a new _strobemer_ design for aligning and requires its own way of indexing the genome.
Expand Down
20 changes: 10 additions & 10 deletions Workflows/SV/leviathan.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,16 +63,16 @@ harpy sv leviathan --threads 20 -g genome.fasta Align/bwa
In addition to the [!badge variant="info" corners="pill" text="common runtime options"](/commonoptions.md), the [!badge corners="pill" text="sv leviathan"] module is configured using these command-line arguments:

{.compact}
| argument | short name | default | required | description |
| :--------------- | :--------: | :-----: | :------: | :----------------------------------------------------------------------------------- |
| `INPUTS` | | | ‼️ | Files or directories containing [input BAM files](/commonoptions.md#input-arguments) |
| `--contigs` | | | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | | | Additional naibr arguments, in quotes |
| `--genome` | `-g` | | ‼️ | Genome assembly that was used to create alignments |
| `--iterations` | `-i` | `50` | | Number of iterations to perform through index (reduces memory) |
| `--min-barcodes` | `-b` | `2` | | Minimum number of barcode overlaps supporting candidate SV |
| `--min-sv` | `-m` | `1000` | | Minimum size of SV to detect |
| `--populations` | `-p` | | | Tab-delimited file of sample\<*tab*\>group |
| argument | short name | default | description |
| :--------------- | :--------: | :-----: | :--------------------------------------------------------------------------------------------------------------------------- |
| `INPUTS` | | | [!badge variant="info" text="required"] Files or directories containing [input BAM files](/commonoptions.md#input-arguments) |
| `--contigs` | | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | | Additional naibr arguments, in quotes |
| `--genome` | `-g` | | [!badge variant="info" text="required"] Genome assembly that was used to create alignments |
| `--iterations` | `-i` | `50` | Number of iterations to perform through index (reduces memory) |
| `--min-barcodes` | `-b` | `2` | Minimum number of barcode overlaps supporting candidate SV |
| `--min-sv` | `-m` | `1000` | Minimum size of SV to detect |
| `--populations` | `-p` | | Tab-delimited file of sample\<*tab*\>group |

### Single-sample variant calling
When **not** using a population grouping file via `--populations`, variants will be called per-sample.
Expand Down
24 changes: 12 additions & 12 deletions Workflows/SV/naibr.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,18 +63,18 @@ harpy sv naibr --threads 20 --genome genome.fasta --vcf Variants/data.vcf.gz Ali
In addition to the [!badge variant="info" corners="pill" text="common runtime options"](/commonoptions.md), the [!badge corners="pill" text="sv naibr"] module is configured using these command-line arguments:

{.compact}
| argument | short name | default | required | description |
| :-------------------- | :--------: | :------: | :------: | :----------------------------------------------------------------------------------- |
| `INPUTS` | | | ‼️ | Files or directories containing [input BAM files](/commonoptions.md#input-arguments) |
| `--contigs` | | | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | | | Additional naibr arguments, in quotes |
| `--genome` | `-g` | | ‼️ | Genome assembly for phasing bam files |
| `--min-barcodes` | `-b` | `2` | | Minimum number of barcode overlaps supporting candidate SV |
| `--min-quality` | `-q` | `30` | | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--min-sv` | `-n` | `1000` | | Minimum size of SV to detect |
| `--molecule-distance` | `-m` | `100000` | | Base-pair distance threshold to separate molecules |
| `--populations` | `-p` | | | Tab-delimited file of sample\<*tab*\>group |
| `--vcf` | `-v` | | ❗ | Phased vcf file for phasing bam files ([see below](#optional-vcf-file)) |
| argument | short name | default | description |
| :-------------------- | :--------: | :------: | :---------------------------------------------------------------------------------------------------------------------------- |
| `INPUTS` | | | [!badge variant="info" text="required"] Files or directories containing [input BAM files](/commonoptions.md#input-arguments) |
| `--contigs` | | | [Contigs to plot](/commonoptions.md#--contigs) in the report |
| `--extra-params` | `-x` | | Additional naibr arguments, in quotes |
| `--genome` | `-g` | | [!badge variant="info" text="required"] Genome assembly for phasing bam files |
| `--min-barcodes` | `-b` | `2` | Minimum number of barcode overlaps supporting candidate SV |
| `--min-quality` | `-q` | `30` | Minimum `MQ` (SAM mapping quality) to pass filtering |
| `--min-sv` | `-n` | `1000` | Minimum size of SV to detect |
| `--molecule-distance` | `-m` | `100000` | Base-pair distance threshold to separate molecules |
| `--populations` | `-p` | | Tab-delimited file of sample\<*tab*\>group |
| `--vcf` | `-v` | | [!badge variant="info" text="conditionally required"] Phased vcf file for phasing bam files ([see below](#optional-vcf-file)) |

### Molecule distance
The `--molecule-distance` option is used to let the program determine how far apart alignments on a contig with the same
Expand Down
Loading

0 comments on commit 25a4c4d

Please sign in to comment.