chore: Merge branch 'main' into filteraligned

CCBR · Oct 23, 2023 · 3abf4a5 · 3abf4a5
2 parents 6d1f8d1 + 92491d5
commit 3abf4a5
Show file tree

Hide file tree

Showing 6 changed files with 24 additions and 24 deletions.
diff --git a/modules/CCBR/custom/bam_to_fastq/main.nf → modules/CCBR/custom/bam2fastq/main.nf b/modules/CCBR/custom/bam_to_fastq/main.nf → 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 → modules/CCBR/custom/bam2fastq/meta.yml b/modules/CCBR/custom/bam_to_fastq/meta.yml → 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/.../modules/CCBR/custom/bam_to_fastq/main.nf → tests/modules/CCBR/custom/bam2fastq/main.nf b/.../modules/CCBR/custom/bam_to_fastq/main.nf → 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/.../CCBR/custom/bam_to_fastq/nextflow.config → ...les/CCBR/custom/bam2fastq/nextflow.config b/.../CCBR/custom/bam_to_fastq/nextflow.config → ...les/CCBR/custom/bam2fastq/nextflow.config
diff --git a/tests/modules/CCBR/custom/bam2fastq/test.yml 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