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Import fasta_fai in main.nf #85

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merged 4 commits into from
Apr 30, 2024
Merged

Import fasta_fai in main.nf #85

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2aef0e2
impot fasta_fai
asp8200 Mar 15, 2024
bd05f59
remove redundant definition of fasta_fai
asp8200 Mar 15, 2024
7a5ee93
Remove comment
asp8200 Mar 15, 2024
32487a8
Revert to former msg concerning tests
asp8200 Mar 15, 2024
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7 changes: 2 additions & 5 deletions .github/CONTRIBUTING.md
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Expand Up @@ -26,11 +26,8 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:

```bash
nf-test test --profile debug,test,docker --verbose
```
You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
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5 changes: 1 addition & 4 deletions main.nf
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Expand Up @@ -27,11 +27,8 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_bamt
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// TODO nf-core: Remove this line if you don't need a FASTA file
// This is an example of how to use getGenomeAttribute() to fetch parameters
// from igenomes.config using `--genome`
params.fasta = getGenomeAttribute('fasta')
// params.fasta_fai = getGenomeAttribute(params, 'fasta_fai')
params.fasta_fai = getGenomeAttribute('fasta_fai')

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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7 changes: 2 additions & 5 deletions workflows/bamtofastq.nf
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Expand Up @@ -10,7 +10,6 @@ include { paramsSummaryMultiqc; softwareVersionsToYAML } from '../subworkflows/n

// Initialize file channels based on params
fasta = params.fasta ? Channel.fromPath(params.fasta).collect() : Channel.value([])
fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : Channel.value([])

// Initialize value channels based on params
chr = params.chr ?: Channel.empty()
Expand Down Expand Up @@ -72,12 +71,9 @@ workflow BAMTOFASTQ {

ch_versions = ch_versions.mix(PREPARE_INDICES.out.versions)

fasta_fai = params.fasta ? params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : PREPARE_INDICES.out.fasta_fai : Channel.value([])

ch_input = PREPARE_INDICES.out.ch_input_indexed

// SUBWORKFLOW: Pre conversion QC and stats

ch_input = PREPARE_INDICES.out.ch_input_indexed
PRE_CONVERSION_QC(
ch_input,
fasta
Expand Down Expand Up @@ -163,6 +159,7 @@ workflow BAMTOFASTQ {
// SUBWORKFLOW: PAIRED-END Alignment to FastQ
//

fasta_fai = params.fasta ? params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : PREPARE_INDICES.out.fasta_fai : Channel.value([])
ALIGNMENT_TO_FASTQ (
conversion_input.ch_paired,
fasta,
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