You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/output.md
+2-2Lines changed: 2 additions & 2 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -105,7 +105,7 @@ of the graph (i.e. the putative cells) and assign a unique ID to each component.
105
105
106
106
From this step and onwards, the output file are in PXL format. This is a custom format used by pixelator to make PNA data easier
107
107
to work with. Internally it used duckdb to store the data. For more information on the PXL format, please refer to
108
-
the [pixelator documentation](https://software.pixelgen.com/pixelator/outputs/pxl-format/).
108
+
the [pixelator documentation](https://software.pixelgen.com/pixelator/outputs/pxl-file/).
109
109
110
110
<detailsmarkdown="1">
111
111
<summary>Output files</summary>
@@ -248,7 +248,7 @@ The output from this step will be placed in the output folder root.
248
248
249
249
</details>
250
250
251
-
[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
251
+
[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
Copy file name to clipboardExpand all lines: docs/usage.md
+91-82Lines changed: 91 additions & 82 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -4,7 +4,66 @@
4
4
5
5
> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
6
6
7
-
## Introduction
7
+
## Quick start
8
+
9
+
The typical command for running the pipeline is as follows:
10
+
11
+
```bash
12
+
nextflow run nf-core/pixelator \
13
+
-profile docker,cells_8k \
14
+
--input ./samplesheet.csv \
15
+
--outdir ./results \
16
+
--technology proxiome-v2
17
+
```
18
+
19
+
This will launch the pipeline with the `docker` configuration profile, and resource configurations
20
+
for 8000 cells. If you have samples with 1000 cells as input, pick the `cells_1k` profile instead.
21
+
See below for more information about profiles.
22
+
23
+
Note that the pipeline will create the following files in your working directory:
24
+
25
+
```bash
26
+
work # Directory containing the nextflow working files
27
+
<OUTDIR># Finished results in specified location (defined with --outdir)
28
+
.nextflow_log # Log file from Nextflow
29
+
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
30
+
```
31
+
32
+
## Parameters
33
+
34
+
nf-core/pixelator can take a wide range of parameters, three of which are mandatory:
35
+
36
+
-`--input`: the path to your samplesheet
37
+
-`--outdir`: the directory where the `.pxl` files and the experiment summary will be saved.
38
+
-`--technology`: the workflow to use to process your data (`proxiome_v1` or `proxiome_v2`), depending on the kit that was used to process the samples.
39
+
40
+
Detailed documentation about each parameter can be found at [https://nf-co.re/pixelator/parameters/](https://nf-co.re/pixelator/parameters/).
41
+
42
+
If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
43
+
44
+
Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
45
+
46
+
> [!WARNING]
47
+
> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args).
48
+
49
+
The above pipeline run specified with a params file in yaml format:
50
+
51
+
```bash
52
+
nextflow run nf-core/pixelator -profile docker,cells_8k -params-file params.yaml
53
+
```
54
+
55
+
with:
56
+
57
+
```yaml title="params.yaml"
58
+
input: './samplesheet.csv'
59
+
outdir: './results/'
60
+
<...>
61
+
```
62
+
63
+
You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
64
+
65
+
> [!NOTE]
66
+
> By default, processes from nf-core/pixelator will use the path defined in `TMPDIR` to store temporary file. If this variable is not defined, they will fallback to `/tmp`.
8
67
9
68
## Samplesheet input
10
69
@@ -15,37 +74,16 @@ Use this parameter to specify its location.
15
74
--input '[path to samplesheet file]'
16
75
```
17
76
18
-
We provide example samplesheets for [Proxiome v1 data](../assets/samplesheet_proxiome_v1.csv)
19
-
and [Proxiome v2 data](../assets/samplesheet_proxiome_v2.csv), that can be used as a template to
77
+
We provide example samplesheets for [Proxiome v1 data](../assets/example_samplesheet_proxiome_v1.csv)
78
+
and [Proxiome v2 data](../assets/example_samplesheet_proxiome_v2.csv), that can be used as a template to
20
79
create your own samplesheet.
21
80
22
81
### Format
23
82
24
83
The samplesheet is a CSV or TSV formatted file with a few required and some optional columns.
25
84
You can export to CSV from spreadsheet programs such as Microsoft Excel, Google Sheets and LibreOffice Calc.
26
85
27
-
Following table provides an overview of all possible columns in the samplesheet.
28
-
The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 5 columns
29
-
to match those defined in the table below.
30
-
31
-
> [!WARNING]
32
-
> It is important that you select a panel file that matches the kit lot version you are
33
-
> using for your experiment. Using a mismatched panel file will lead to incorrect antibody
34
-
> assignments and erroneous results.
35
-
>
36
-
> An updated list of which panel files correspond to which kit lot versions can be found
37
-
> on the [Pixelgen Technologies website](https://www.pixelgen.com/panel-file-for-data-processing/)
38
-
39
-
Below is an example of a simple samplesheet with two samples.
@@ -64,6 +102,22 @@ One of them has to be specified.
64
102
65
103
The pipeline will auto-detect whether a sample is single- or paired-end based on if both `fastq_1` and `fastq_2` or only `fastq_1` is present in the samplesheet.
66
104
105
+
> [!WARNING]
106
+
> It is important that you select a panel file that matches the kit lot version you are
107
+
> using for your experiment. Using a mismatched panel file will lead to incorrect antibody
108
+
> assignments and erroneous results.
109
+
>
110
+
> An updated list of which panel files correspond to which kit lot versions can be found
111
+
> on the [Pixelgen Technologies website](https://www.pixelgen.com/panel-file-for-data-processing/)
112
+
113
+
Below is an example of a simple samplesheet with two samples.
This will launch the pipeline with the `docker` configuration profile, and resource configurations
180
-
for 8000 cells. If you have samples with 1000 cells as input, pick the `cells_1k` profile instead.
181
-
See below for more information about profiles.
182
-
183
-
Note that the pipeline will create the following files in your working directory:
184
-
185
-
```bash
186
-
work # Directory containing the nextflow working files
187
-
<OUTDIR># Finished results in specified location (defined with --outdir)
188
-
.nextflow_log # Log file from Nextflow
189
-
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
190
-
```
191
-
192
-
If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
193
-
194
-
Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
195
-
196
-
> [!WARNING]
197
-
> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args).
198
-
199
-
The above pipeline run specified with a params file in yaml format:
200
-
201
-
```bash
202
-
nextflow run nf-core/pixelator -profile docker,cells_8k -params-file params.yaml
203
-
```
204
-
205
-
with:
206
-
207
-
```yaml title="params.yaml"
208
-
input: './samplesheet.csv'
209
-
outdir: './results/'
210
-
<...>
211
-
```
212
-
213
-
You can find an extensive example of a `params.yaml` file with all options and
214
-
documentation in comments [here](../assets/params-file.yml).
215
-
You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
216
-
217
-
> [!NOTE]
218
-
> By default, processes from nf-core/pixelator will use the path defined in `TMPDIR` to store temporary file. If this variable is not defined, they will fallback to `/tmp`.
225
+
Alternatively, these panel files can be downloaded from the [`pixelator`
0 commit comments