Skip to content

Commit

Permalink
Merge pull request #19 from CCBR/bam2fastq
Browse files Browse the repository at this point in the history
refactor: rename bam_to_fastq -> bam2fastq
  • Loading branch information
kelly-sovacool authored Oct 23, 2023
2 parents e467a9c + 4d203b8 commit 92491d5
Show file tree
Hide file tree
Showing 7 changed files with 27 additions and 27 deletions.
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
process BAM_TO_FASTQ {
process 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' }"
Expand Down
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: bam_to_fastq
name: bam2fastq
description: |
The module converts a BAM file to FASTQ format.
It uses samtools bam2fq if reads are single end,
Expand Down
6 changes: 3 additions & 3 deletions tests/config/pytest_modules.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,9 @@ bwa/mem:
- modules/CCBR/bwa/mem/**
- tests/modules/CCBR/bwa/mem/**

custom/bam_to_fastq:
- modules/CCBR/custom/bam_to_fastq/**
- tests/modules/CCBR/custom/bam_to_fastq/**
custom/bam2fastq:
- modules/CCBR/custom/bam2fastq/**
- tests/modules/CCBR/custom/bam2fastq/**

cutadapt:
- modules/CCBR/cutadapt/**
Expand Down
Original file line number Diff line number Diff line change
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 { BAM_TO_FASTQ } from '../../../../../modules/CCBR/custom/bam_to_fastq/main.nf'
include { 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 )
BAM_TO_FASTQ( BWA_MEM.out.bam )
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 )
BAM_TO_FASTQ( BWA_MEM.out.bam )
BAM2FASTQ( BWA_MEM.out.bam )
}
19 changes: 19 additions & 0 deletions tests/modules/CCBR/custom/bam2fastq/test.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
- name: custom bam2fastq test_bam2fastq_single
command: nextflow run ./tests/modules/CCBR/custom/bam2fastq -entry test_bam2fastq_single -c ./tests/config/nextflow.config
tags:
- custom/bam2fastq
- custom
files:
- path: output/bam2fastq/test.R1.fastq.gz
- path: output/bwa/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
19 changes: 0 additions & 19 deletions tests/modules/CCBR/custom/bam_to_fastq/test.yml

This file was deleted.

0 comments on commit 92491d5

Please sign in to comment.