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Add missing step
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Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
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mribeirodantas committed Jun 25, 2024
1 parent 821799b commit 936bcdf
Showing 1 changed file with 18 additions and 3 deletions.
21 changes: 18 additions & 3 deletions docs/hello_nextflow/03_hello_gatk.md
Original file line number Diff line number Diff line change
Expand Up @@ -367,7 +367,22 @@ GATK_HAPLOTYPECALLER(
SAMTOOLS_INDEX.out,
```

#### 3.6. Run the workflow to verify it works correctly on all three samples now
#### 3.6 Update the channel factory to read from a list

_Before:_

```groovy title="hello-gatk.nf"
// Create input channel (single file via CLI parameter)
reads_ch = Channel.of(params.reads_bam)
```

_After:_
```groovy title="hello-gatk.nf"
// Create input channel (multiple files via CLI parameter)
reads_ch = Channel.fromList(params.reads_bam)
```

#### 3.7. Run the workflow to verify it works correctly on all three samples now

```bash
nextflow run hello-gatk.nf -ansi-log false
Expand Down Expand Up @@ -431,8 +446,8 @@ params.reads_bam = "${projectDir}/data/sample_bams.txt"
_Before:_

```groovy title="hello-gatk.nf"
// Create input channel
reads_ch = Channel.of(params.reads_bam)
// Create input channel (single file via CLI parameter)
reads_ch = Channel.fromList(params.reads_bam)
```

_After:_
Expand Down

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