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Tiny update of docs #490

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Tiny update of docs #490

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543b7d2
Fixing typo in README
asp8200 Jun 11, 2024
204289c
Adding profile to nf run-cmds
asp8200 Jun 11, 2024
488dc82
Update changelog
asp8200 Jun 11, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed

- Fixed some Nextflow run-commands in the docs [#490](https://github.com/nf-core/rnafusion/pull/490)

### Removed

## v3.0.2 - [2024-04-10]
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6 changes: 2 additions & 4 deletions README.md
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Expand Up @@ -76,8 +76,7 @@ First, build the references:

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
-profile test \
-profile test,<docker/singularity/.../institute> \
--outdir <OUTDIR>\
--build_references \
-stub
Expand All @@ -87,8 +86,7 @@ Then perform the analysis:

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
-profile test \
-profile test,<docker/singularity/.../institute> \
--outdir <OUTDIR>\
-stub
```
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12 changes: 12 additions & 0 deletions docs/usage.md
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Expand Up @@ -31,6 +31,7 @@ The rnafusion pipeline needs references for the fusion detection tools, so downl

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--build_references --all \
--cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
--genomes_base <PATH/TO/REFERENCES> \
Expand All @@ -41,6 +42,7 @@ References for each tools can also be downloaded separately with:

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--build_references --<tool1> --<tool2> ... \
--cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
--genomes_base <PATH/TO/REFERENCES> \
Expand All @@ -59,6 +61,7 @@ Use credentials from QIAGEN and add `--qiagen`

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--build_references --<tool1> --<tool2> ... \
--cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
--genomes_base <PATH/TO/REFERENCES> \
Expand All @@ -75,6 +78,7 @@ If process `FUSIONREPORT_DOWNLOAD` times out, it could be due to network restric

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--build_references \
--cosmic_username <EMAIL> --cosmic_passwd <PASSWORD> \
--fusionreport \
Expand Down Expand Up @@ -134,6 +138,7 @@ The pipeline can either be run using all fusion detection tools or specifying in

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--all \
--input <SAMPLE_SHEET.CSV> \
--genomes_base <PATH/TO/REFERENCES> \
Expand All @@ -144,6 +149,7 @@ To run only a specific detection tool use: `--tool`:

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--<tool1> --<tool2> ... \
--input <SAMPLE_SHEET.CSV> \
--genomes_base <PATH/TO/REFERENCES> \
Expand Down Expand Up @@ -200,6 +206,7 @@ When the flag `--fastp_trim` is used, `fastp` is used to provide all tools with

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--<tool1> --<tool2> ... \
--input <SAMPLE_SHEET.CSV> \
--genomes_base <PATH/TO/REFERENCES> \
Expand All @@ -213,6 +220,7 @@ nextflow run nf-core/rnafusion \

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--<tool1> --<tool2> ... \
--input <SAMPLE_SHEET.CSV> \
--genomes_base <PATH/TO/REFERENCES> \
Expand All @@ -226,6 +234,7 @@ nextflow run nf-core/rnafusion \

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--<tool1> --<tool2> ... \
--input <SAMPLE_SHEET.CSV> \
--genomes_base <PATH/TO/REFERENCES> \
Expand All @@ -246,6 +255,7 @@ FusionInspector can be run as a standalone with:

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--fusioninspector_only \
--fusioninspector_fusions <PATH_TO_CUSTOM_FUSION_FILE> \
--input <SAMPLE_SHEET.CSV> \
Expand All @@ -263,6 +273,7 @@ GENE3--GENE4

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--skip_qc \
--all OR <--tool>
--input <SAMPLE_SHEET.CSV> \
Expand All @@ -276,6 +287,7 @@ This will skip all QC-related processes (picard metrics collection)

```bash
nextflow run nf-core/rnafusion \
-profile <docker/singularity/.../institute> \
--skip_vis \
--all OR <--tool>
--input <SAMPLE_SHEET.CSV> \
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