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Merge pull request nf-core#169 from mashehu/update-file-refs
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add file names to code examples
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mashehu authored Jul 9, 2024
2 parents 5ca8c65 + 8136045 commit d94bab6
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8 changes: 2 additions & 6 deletions README.md
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Expand Up @@ -79,18 +79,14 @@ For crispr screening:
First, prepare a samplesheet with your input data that looks as follows:

`samplesheet.csv`:

```csv
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2,reference,protospacer,template
SAMPLE1,SAMPLE1_R1.fastq.gz,SAMPLE1_R2.fastq.gz,ACTG,ACTG,ACTG
```

or

`samplesheet.csv`:

```csv
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2,condition
SAMPLE1,SAMPLE1_R1.fastq.gz,SAMPLE1_R2.fastq.gz,control
```
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -52,7 +52,7 @@ nextflow run nf-core/crisprseq -profile docker -params-file params.yaml

with `params.yaml` containing:

```yaml
```yaml title="params.yaml"
input: './samplesheet.csv'
outdir: './results/'
genome: 'GRCh37'
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2 changes: 1 addition & 1 deletion docs/usage/screening.md
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Expand Up @@ -27,7 +27,7 @@ If you wish to input a raw count or normalized table, you can skip the sampleshe

The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 4 columns to match those defined in the table below.

```console
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2,condition
SRR8983579,SRR8983579.small.fastq.gz,,control
SRR8983580,SRR8983580.small.fastq.gz,,treatment
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7 changes: 3 additions & 4 deletions docs/usage/targeted.md
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Expand Up @@ -24,7 +24,7 @@ You will need to create a samplesheet with information about the samples you wou

The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes _(see section below for an explanation of samplesheet columns)_:

```console
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2,reference,protospacer,template
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
Expand All @@ -37,7 +37,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th

A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 3 samples, where `chr6` is single-end and has a template sequence _(this is a reduced samplesheet, please refer to the [pipeline example samplesheet](https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata-edition/samplesheet_test_full.csv) to see the full version)_.

```console
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2,reference,protospacer,template
hCas9-TRAC-a,hCas9-TRAC-a_R1.fastq.gz,hCas9-TRAC-a_R2.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
hCas9-AAVS1-a,hCas9-AAVS1-a_R1.fastq.gz,hCas9-AAVS1-a_R2.fastq.gz,GCT...CCT,GGGGCCACTAGGGACAGGAT,
Expand Down Expand Up @@ -108,8 +108,7 @@ Please refer to the original [CRISPR-Analytics](https://doi.org/10.1371/journal.

In order to customise such parameters, you can override the arguments given to `minimap2` by creating a configuration file and provide it to your nextflow run with `-c`:

```groovy
// Custom config file custom.config
```groovy title="custom.config"
process {
withName: MINIMAP2_ALIGN_ORIGINAL {
ext.args = '-A 29 -B 17 -O 25 -E 2'
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