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Merge pull request #54 from nf-core/move-params
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 All the docs removed from usage.md and moved to json schema
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@sk-sahu
sk-sahu committed Mar 26, 2021
2 parents c7f237f + 647b439 commit 1156161
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199 changes: 8 additions & 191 deletions docs/usage.md
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Expand Up @@ -83,95 +83,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- A profile with a complete configuration for automated testing
- Includes links to test data so needs no other parameters

### `--reads`

Use this to specify the location of your input FastQ files. For example:

```bash
--reads 'path/to/data/sample_*_{1,2}.fastq'
```

Please note the following requirements:

1. The path must be enclosed in quotes
2. The path must have at least one `*` wildcard character
3. When using the pipeline with paired end data, the path must use `{1,2}` notation to specify read pairs.

If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`

### `--aligner` (Required)

The workflow can handle three types of methods:

- Kallisto/Bustools
- Salmon Alevin + AlevinQC
- STARsolo

To choose which one to use, please specify either `alevin`, `star` or `kallisto` as a parameter option for `--aligner`. By default, the pipeline runs the `alevin` option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.

#### Alevin

##### `--salmon_index`

This can be used to specify a precomputed Salmon index in the pipeline, in order to skip the generation of required indices by Salmon itself.

##### `--txp2gene`

This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.

> This is not the same as the `kallisto_gene_map` parameter down below and is only used by the Salmon Alevin workflow.
#### STARSolo

##### `--star_index`

Specify a path to the precomputed STAR index.

> NB: This has to be computed with STAR Version 2.7 or later, as STARsolo was only first supported by STAR Version 2.7.
#### Kallisto | BUStools

##### `--bustools_correct`

If set to false, skip the correct steps after mapping with Kallisto.

##### `--skip_bustools`

When supplied, skip BUStools entirely.

##### `--kallisto_gene_map`

Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.

##### `--kallisto_index`

Specify a path to the precomputed Kallisto index.

### Cellular barcodes

#### `--type` to specify droplet type (Required)

Currently, only 10X Genomics' chromium chemistry is supported. Drop-Seq, inDrop, etc may be supported in the future.

#### `--chemistry` (using cellranger barcodes) (Required)

To specify which chemistry (and thus barcode whitelist) to use, use the `--chemistry` flag. For example, to specify V3 chemistry (the default, as it is compatible with V2), use `--chemistry V3`.

These files were copied out of 10x Genomics' [cellranger](https://github.com/10XGenomics/cellranger) `cellranger/lib/python/cellranger/barcodes`, in some cases gzipped for simplicity across versions, and copied to `assets/whitelist`.

- V1: `737K-april-2014_rc.txt` --> gzipped --> `10x_V1_barcode_whitelist.txt.gz`
- V2: `737K-august-2016.txt` --> gzipped --> `10x_V2_barcode_whitelist.txt.gz`
- V3: `3M-february-2018.txt.gz` --> `10x_V3_barcode_whitelist.txt.gz`

#### `--barcode_whitelist` for custom barcode whitelist

If not using the 10X Genomics platform, a custom barcode whitelist can be used with `--barcode_whitelist`.

## Reference genomes

The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.

### `--genome` (using iGenomes)
### `-resume`

Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.

Expand All @@ -185,6 +97,8 @@ Specify the path to a specific config file (this is a core Nextflow command). Se

Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.

Whilst these default requirements will hopefully work for most people with most data, you may find that you want to customise the compute resources that the pipeline requests. You can do this by creating a custom config file. For example, to give the workflow process `star` 32GB of memory, you could use the following config:

```nextflow
process {
withName: star {
Expand All @@ -193,49 +107,7 @@ process {
}
```

### `--fasta`

If you prefer, you can specify the full path to your reference genome when you run the pipeline:

```bash
--fasta '[path to Fasta reference]'
```

> Note that you need to specify either a `--genome` or `--fasta` when running the STARsolo workflow. The Kallisto and Alevin workflows can utilize a `--transcript_fasta` instead, whereas STAR needs a genomic fasta file as input in all cases.
### `--gtf`

Specify a valid GTF file for the workflow here.

### `--transcript_fasta`

If you intend to skip the generation of a transcriptomic fasta file, you can use this parameter to supply a transcriptomic fasta file here. If you don't specify this, it will be automatically generated from the supplied genomics fasta file utilizing the GTF annotation subsequently.

### `--save_reference`

Specify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.

### `--igenomes_ignore`

Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.

## Job resources

### Automatic resubmission

Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.

### Custom resource requests

Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files hosted at [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.

If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition below). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.

If you have any questions or issues please send us a message on [Slack](https://nfcore.slack.com/channels/scrnaseq/).

## AWS Batch specific parameters

Running the pipeline on AWS Batch requires a couple of specific parameters to be set according to your AWS Batch configuration. Please use the `-awsbatch` profile and then specify all of the following parameters.
See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information.

If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition above). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.

Expand All @@ -247,68 +119,13 @@ Nextflow handles job submissions and supervises the running jobs. The Nextflow p

The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file.

The [AWS CLI](https://www.nextflow.io/docs/latest/awscloud.html#aws-cli-installation) path in your custom AMI. Default: `/home/ec2-user/miniconda/bin/aws`.
The AWS region to run your job in. Default is set to `eu-west-1` but can be adjusted to your needs.
Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time.
Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs).

#### Nextflow memory requirements

## Other command line parameters

### `--outdir`

The output directory where the results will be saved.

### `--email`

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.

### `--email_on_fail`

This works exactly as with `--email`, except emails are only sent if the workflow is not successful.

### `--max_multiqc_email_size`

Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB).

### `-name`

Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.

This is used in the MultiQC report (if not default) and in the summary HTML / e-mail (always).

**NB:** Single hyphen (core Nextflow option)

### `-resume`

Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously.

You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.

**NB:** Single hyphen (core Nextflow option)

### `-c`

Specify the path to a specific config file (this is a core NextFlow command).

**NB:** Single hyphen (core Nextflow option)

Note - you can use this to override pipeline defaults.

### `--custom_config_version`

Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.

```bash
## Download and use config file with following git commid id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
```

### `--custom_config_base`

If you're running offline, nextflow will not be able to fetch the institutional config files
from the internet. If you don't need them, then this is not a problem. If you do need them,
you should download the files from the repo and tell nextflow where to find them with the
`custom_config_base` option. For example:
In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):

```bash
NXF_OPTS='-Xms1g -Xmx4g'
Expand Down
54 changes: 34 additions & 20 deletions nextflow_schema.json
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Expand Up @@ -20,7 +20,8 @@
"input_paths": {
"type": "string",
"hidden": true,
"description": "Input FastQ files path in array format"
"description": "Input FastQ files path in array format",
"fa_icon": "fas fa-dna"
},
"outdir": {
"type": "string",
Expand All @@ -45,25 +46,31 @@
"properties": {
"type": {
"type": "string",
"description": "Name of droplet technology (Currently supported: 10x)",
"description": "Name of droplet technology (Currently supported: 10x, Drop-Seq, inDrop, etc may be supported in the future.)",
"fa_icon": "fas fa-align-center",
"default": "10x"
},
"chemistry": {
"type": "string",
"description": "Version of 10x chemistry",
"default": "V3"
"default": "V3",
"help_text": "To specify which chemistry (and thus barcode whitelist) to use, use the `--chemistry` flag. For example, to specify V3 chemistry (the default, as it is compatible with V2), use `--chemistry V3`.\n\nThese files were copied out of 10x Genomics' [cellranger](https://github.com/10XGenomics/cellranger) `cellranger/lib/python/cellranger/barcodes`, in some cases gzipped for simplicity across versions, and copied to `assets/whitelist`.\n\n- V1: `737K-april-2014_rc.txt` --> gzipped --> `10x_V1_barcode_whitelist.txt.gz`\n- V2: `737K-august-2016.txt` --> gzipped --> `10x_V2_barcode_whitelist.txt.gz`\n- V3: `3M-february-2018.txt.gz` --> `10x_V3_barcode_whitelist.txt.gz`",
"fa_icon": "fas fa-atom"
},
"barcode_whitelist": {
"type": "string",
"description": "Custom file of whitelisted barcodes"
"description": "If not using the 10X Genomics platform, a custom barcode whitelist can be used with `--barcode_whitelist`.",
"fa_icon": "fas fa-barcode"
},
"aligner": {
"type": "string",
"description": "Name of the tool to use for scRNA (pseudo-) alignment. Available are: \"alevin\", \"star\", \"kallisto\". Default 'alevin'.",
"default": "alevin"
"default": "alevin",
"help_text": "The workflow can handle three types of methods:\n\n- Kallisto/Bustools\n- Salmon Alevin + AlevinQC\n- STARsolo\n\nTo choose which one to use, please specify either `alevin`, `star` or `kallisto` as a parameter option for `--aligner`. By default, the pipeline runs the `alevin` option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.",
"fa_icon": "fas fa-align-center"
}
}
},
"fa_icon": "fas fa-terminal"
},
"reference_genome_options": {
"title": "Reference genome options",
Expand Down Expand Up @@ -99,11 +106,13 @@
},
"transcript_fasta": {
"type": "string",
"description": "A cDNA fastq file"
"description": "A cDNA fastq file",
"fa_icon": "fas fa-dna"
},
"gtf": {
"type": "string",
"description": "Reference GTF annotation file"
"description": "Reference GTF annotation file",
"fa_icon": "fas fa-code-branch"
},
"save_reference": {
"type": "string",
Expand All @@ -120,11 +129,14 @@
"properties": {
"salmon_index": {
"type": "string",
"description": "Path to Salmon index"
"description": "This can be used to specify a precomputed Salmon index in the pipeline, in order to skip the generation of required indices by Salmon itself.",
"fa_icon": "fas fa-fish"
},
"txp2gene": {
"type": "string",
"description": "Path to transcript to gene mapping file"
"description": "Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.",
"help_text": "> This is not the same as the `kallisto_gene_map` parameter down below and is only used by the Salmon Alevin workflow.",
"fa_icon": "fas fa-map-marked-alt"
}
}
},
Expand All @@ -136,7 +148,9 @@
"properties": {
"star_index": {
"type": "string",
"description": "Path to STARSolo index"
"description": "Specify a path to the precomputed STAR index.",
"help_text": "> NB: This has to be computed with STAR Version 2.7 or later, as STARsolo was only first supported by STAR Version 2.7.",
"fa_icon": "fas fa-asterisk"
}
},
"fa_icon": "fas fa-star"
Expand All @@ -150,19 +164,23 @@
"properties": {
"kallisto_gene_map": {
"type": "string",
"description": "A gene map used for bustools correction of BUS files created by Kallisto"
"description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.",
"fa_icon": "fas fa-fish"
},
"bustools_correct": {
"type": "boolean",
"description": "Perform BUS correction step in BUSTools"
"description": "If set to false, skip the correct steps after mapping with Kallisto.",
"fa_icon": "fas fa-bus-alt"
},
"skip_bustools": {
"type": "boolean",
"description": "Skip BUStools entirely in workflow"
"description": "Skip BUStools entirely in workflow",
"fa_icon": "fas fa-forward"
},
"kallisto_index": {
"type": "string",
"description": "Supply precomputed Kallisto index to pipeline"
"description": "Specify a path to the precomputed Kallisto index.",
"fa_icon": "fas fa-fish"
}
}
},
Expand All @@ -173,10 +191,6 @@
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"name": {
"type": "string",
"description": "Name of the pipeline run"
},
"help": {
"type": "boolean",
"description": "Display help text.",
Expand Down Expand Up @@ -378,4 +392,4 @@
"$ref": "#/definitions/institutional_config_options"
}
]
}
}

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