diff --git a/modules/CCBR/custom/bam_to_fastq/main.nf b/modules/CCBR/custom/bam2fastq/main.nf similarity index 98% rename from modules/CCBR/custom/bam_to_fastq/main.nf rename to modules/CCBR/custom/bam2fastq/main.nf index 65dbc0b..2ea65f3 100644 --- a/modules/CCBR/custom/bam_to_fastq/main.nf +++ b/modules/CCBR/custom/bam2fastq/main.nf @@ -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' }" diff --git a/modules/CCBR/custom/bam_to_fastq/meta.yml b/modules/CCBR/custom/bam2fastq/meta.yml similarity index 98% rename from modules/CCBR/custom/bam_to_fastq/meta.yml rename to modules/CCBR/custom/bam2fastq/meta.yml index e5c868e..3628629 100644 --- a/modules/CCBR/custom/bam_to_fastq/meta.yml +++ b/modules/CCBR/custom/bam2fastq/meta.yml @@ -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, diff --git a/tests/modules/CCBR/custom/bam_to_fastq/main.nf b/tests/modules/CCBR/custom/bam2fastq/main.nf similarity index 88% rename from tests/modules/CCBR/custom/bam_to_fastq/main.nf rename to tests/modules/CCBR/custom/bam2fastq/main.nf index 464c5a1..4bc7035 100644 --- a/tests/modules/CCBR/custom/bam_to_fastq/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 { 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 @@ -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 ) } // @@ -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 ) } diff --git a/tests/modules/CCBR/custom/bam_to_fastq/nextflow.config b/tests/modules/CCBR/custom/bam2fastq/nextflow.config similarity index 100% rename from tests/modules/CCBR/custom/bam_to_fastq/nextflow.config rename to tests/modules/CCBR/custom/bam2fastq/nextflow.config diff --git a/tests/modules/CCBR/custom/bam2fastq/test.yml b/tests/modules/CCBR/custom/bam2fastq/test.yml new file mode 100644 index 0000000..2eb80da --- /dev/null +++ b/tests/modules/CCBR/custom/bam2fastq/test.yml @@ -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 diff --git a/tests/modules/CCBR/custom/bam_to_fastq/test.yml b/tests/modules/CCBR/custom/bam_to_fastq/test.yml deleted file mode 100644 index 513f439..0000000 --- a/tests/modules/CCBR/custom/bam_to_fastq/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: custom bam_to_fastq test_bam2fastq_single - command: nextflow run ./tests/modules/CCBR/custom/bam_to_fastq -entry test_bam2fastq_single -c ./tests/config/nextflow.config - tags: - - custom/bam_to_fastq - - custom - files: - - path: output/bam/test.R1.fastq.gz - - path: output/bwa/versions.yml - -- name: custom bam_to_fastq test_bam2fastq_paired - command: nextflow run ./tests/modules/CCBR/custom/bam_to_fastq -entry test_bam2fastq_paired -c ./tests/config/nextflow.config - tags: - - custom/bam_to_fastq - - custom - files: - - path: output/bam/test.R1.fastq.gz - - path: output/bam/test.R2.fastq.gz - - path: output/bam/test.unpaired.fastq.gz - - path: output/bwa/versions.yml