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refactor: name bam2fastq process for nf-core schema #22

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merged 2 commits into from
Oct 24, 2023
Merged

refactor: name bam2fastq process for nf-core schema #22

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b63a3f5
refactor: name bam2fastq process for nf-core schema
kelly-sovacool Oct 23, 2023
465ffda
docs: update changelog
kelly-sovacool Oct 23, 2023
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
- bwa/index
- bwa/mem
- also runs samtools sort & outputs index in bai format. (#12)
- custom/bam_to_fastq (#14)
- custom/bam2fastq (#14,#22)
- cutadapt (#11)
- khmer/uniquekmers (#7)
- picard/samtofastq (#21)
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2 changes: 1 addition & 1 deletion modules/CCBR/custom/bam2fastq/main.nf
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@@ -1,4 +1,4 @@
process BAM2FASTQ {
process CUSTOM_BAM2FASTQ {
tag { meta.id }
label 'process_single'
container "${ meta.single_end ? 'nciccbr/ccbr_ubuntu_base_20.04:v5' : 'nciccbr/ccbr_picard_2.27.5:v1' }"
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2 changes: 1 addition & 1 deletion modules/CCBR/custom/bam2fastq/meta.yml
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@@ -1,4 +1,4 @@
name: bam2fastq
name: custom_bam2fastq
description: |
The module converts a BAM file to FASTQ format.
It uses samtools bam2fq if reads are single end,
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6 changes: 3 additions & 3 deletions tests/modules/CCBR/custom/bam2fastq/main.nf
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Expand Up @@ -4,7 +4,7 @@ nextflow.enable.dsl = 2

include { BWA_INDEX } from '../../../../../modules/CCBR/bwa/index/main.nf'
include { BWA_MEM } from '../../../../../modules/CCBR/bwa/mem/main.nf'
include { BAM2FASTQ } from '../../../../../modules/CCBR/custom/bam2fastq/main.nf'
include { CUSTOM_BAM2FASTQ } from '../../../../../modules/CCBR/custom/bam2fastq/main.nf'

//
// Test with single-end data
Expand All @@ -23,7 +23,7 @@ workflow test_bam2fastq_single {

BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index )
BAM2FASTQ( BWA_MEM.out.bam )
CUSTOM_BAM2FASTQ( BWA_MEM.out.bam )
}

//
Expand All @@ -44,5 +44,5 @@ workflow test_bam2fastq_paired {

BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index )
BAM2FASTQ( BWA_MEM.out.bam )
CUSTOM_BAM2FASTQ( BWA_MEM.out.bam )
}
12 changes: 6 additions & 6 deletions tests/modules/CCBR/custom/bam2fastq/test.yml
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Expand Up @@ -4,16 +4,16 @@
- custom/bam2fastq
- custom
files:
- path: output/bam2fastq/test.R1.fastq.gz
- path: output/bwa/versions.yml
- path: output/custom/test.R1.fastq.gz
- path: output/custom/versions.yml

- name: custom bam2fastq test_bam2fastq_paired
command: nextflow run ./tests/modules/CCBR/custom/bam2fastq -entry test_bam2fastq_paired -c ./tests/config/nextflow.config
tags:
- custom/bam2fastq
- custom
files:
- path: output/bam2fastq/test.R1.fastq.gz
- path: output/bam2fastq/test.R2.fastq.gz
- path: output/bam2fastq/test.unpaired.fastq.gz
- path: output/bwa/versions.yml
- path: output/custom/test.R1.fastq.gz
- path: output/custom/test.R2.fastq.gz
- path: output/custom/test.unpaired.fastq.gz
- path: output/custom/versions.yml