diff --git a/CHANGELOG.md b/CHANGELOG.md index 267ea71..8307cf6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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) diff --git a/modules/CCBR/custom/bam2fastq/main.nf b/modules/CCBR/custom/bam2fastq/main.nf index 2ea65f3..d498fe2 100644 --- a/modules/CCBR/custom/bam2fastq/main.nf +++ b/modules/CCBR/custom/bam2fastq/main.nf @@ -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' }" diff --git a/modules/CCBR/custom/bam2fastq/meta.yml b/modules/CCBR/custom/bam2fastq/meta.yml index 3628629..8485ea1 100644 --- a/modules/CCBR/custom/bam2fastq/meta.yml +++ b/modules/CCBR/custom/bam2fastq/meta.yml @@ -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, diff --git a/tests/modules/CCBR/custom/bam2fastq/main.nf b/tests/modules/CCBR/custom/bam2fastq/main.nf index 4bc7035..3854409 100644 --- a/tests/modules/CCBR/custom/bam2fastq/main.nf +++ b/tests/modules/CCBR/custom/bam2fastq/main.nf @@ -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 @@ -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 ) } // @@ -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 ) } diff --git a/tests/modules/CCBR/custom/bam2fastq/test.yml b/tests/modules/CCBR/custom/bam2fastq/test.yml index 2eb80da..bfaae45 100644 --- a/tests/modules/CCBR/custom/bam2fastq/test.yml +++ b/tests/modules/CCBR/custom/bam2fastq/test.yml @@ -4,8 +4,8 @@ - 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 @@ -13,7 +13,7 @@ - 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