Merge pull request #20 from CCBR/filteraligned

Rename samtools filter aligned module

CHANGELOG.md

@@ -7,5 +7,5 @@
 - custom/bam_to_fastq (#14)
 - cutadapt (#11)
 - khmer/uniquekmers (#7)
-- samtools/filter_aligned (#13)
+- samtools/filteraligned (#13,#20)
   - also runs samtools sort & outputs index in bai format. (#12)

modules/CCBR/samtools/filter_aligned/main.nf → modules/CCBR/samtools/filteraligned/main.nf

@@ -1,5 +1,5 @@
 
-process FILTER_ALIGNED {
+process SAMTOOLS_FILTER_ALIGNED {
     '''
     Given a bam file, filter out reads that aligned.
     '''

modules/CCBR/samtools/filter_aligned/meta.yml → modules/CCBR/samtools/filteraligned/meta.yml

@@ -1,4 +1,4 @@
-name: filter_aligned
+name: samtools_filter_aligned
 description: Filter out aligned reads from a BAM file.
 keywords:
   - bam

tests/config/pytest_modules.yml

@@ -18,6 +18,6 @@ khmer/uniquekmers:
   - modules/CCBR/khmer/uniquekmers/**
   - tests/CCBR/khmer/uniquekmers/**
 
-samtools/filter_aligned:
-  - modules/CCBR/samtools/filter_aligned/**
-  - tests/modules/CCBR/samtools/filter_aligned/**
+samtools/filteraligned:
+  - modules/CCBR/samtools/filteraligned/**
+  - tests/modules/CCBR/samtools/filteraligned/**

tests/modules/CCBR/samtools/filter_aligned/main.nf → tests/modules/CCBR/samtools/filteraligned/main.nf

@@ -2,9 +2,9 @@
 
 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 { FILTER_ALIGNED } from '../../../../../modules/CCBR/samtools/filter_aligned/main.nf'
+include { BWA_INDEX               } from '../../../../../modules/CCBR/bwa/index/main.nf'
+include { BWA_MEM                 } from '../../../../../modules/CCBR/bwa/mem/main.nf'
+include { SAMTOOLS_FILTER_ALIGNED } from '../../../../../modules/CCBR/samtools/filteraligned/main.nf'
 
 //
 // Test with single-end data
@@ -23,7 +23,7 @@ workflow test_filter_aligned_single_end {
 
     BWA_INDEX ( fasta )
     BWA_MEM ( input, BWA_INDEX.out.index )
-    FILTER_ALIGNED( BWA_MEM.out.bam )
+    SAMTOOLS_FILTER_ALIGNED( BWA_MEM.out.bam )
 }
 
 //
@@ -44,5 +44,5 @@ workflow test_filter_aligned_paired_end {
 
     BWA_INDEX ( fasta )
     BWA_MEM ( input, BWA_INDEX.out.index )
-    FILTER_ALIGNED( BWA_MEM.out.bam )
+    SAMTOOLS_FILTER_ALIGNED( BWA_MEM.out.bam )
 }

tests/modules/CCBR/samtools/filter_aligned/test.yml → tests/modules/CCBR/samtools/filteraligned/test.yml

@@ -1,41 +1,41 @@
 - name: samtools filter_aligned test_filter_aligned_single_end
-  command: nextflow run ./tests/modules/CCBR/samtools/filter_aligned -entry test_filter_aligned_single_end -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/modules/CCBR/samtools/filteraligned -entry test_filter_aligned_single_end -c ./tests/config/nextflow.config
   tags:
-    - samtools/filter_aligned
+    - samtools/filteraligned
     - samtools
   files:
     - path: output/bwa/test.bam
       md5sum: 33be5394f2873956dcac679d78c7e559
     - path: output/bwa/test.bam.bai
       md5sum: 9965a3eaf16130c34ded277653b3811f
     - path: output/bwa/versions.yml
-    - path: output/filter/test.unaligned.bam
+    - path: output/samtools/test.unaligned.bam
       md5sum: 60121474c99a15d030b866f459e83a88
-    - path: output/filter/versions.yml
+    - path: output/samtools/versions.yml
 
 - name: samtools filter_aligned test_filter_aligned_paired_end
-  command: nextflow run ./tests/modules/CCBR/samtools/filter_aligned -entry test_filter_aligned_paired_end -c ./tests/config/nextflow.config
+  command: nextflow run ./tests/modules/CCBR/samtools/filteraligned -entry test_filter_aligned_paired_end -c ./tests/config/nextflow.config
   tags:
-    - samtools/filter_aligned
+    - samtools/filteraligned
     - samtools
   files:
     - path: output/bwa/test.bam
       md5sum: 319a128e8959023f52490030b5ee457c
     - path: output/bwa/test.bam.bai
       md5sum: 55703b9bdf1b9816853dd5222c31fc2e
     - path: output/bwa/versions.yml
-    - path: output/filter/test.unaligned.bam
+    - path: output/samtools/test.unaligned.bam
       md5sum: 029fb4355a96008d6b30c0dcc0f210cb
-    - path: output/filter/versions.yml
+    - path: output/samtools/versions.yml
 
 - name: samtools filter_aligned test_filter_aligned_single_end stub
-  command: nextflow run ./tests/modules/CCBR/samtools/filter_aligned -entry test_filter_aligned_single_end -c ./tests/config/nextflow.config -stub
+  command: nextflow run ./tests/modules/CCBR/samtools/filteraligned -entry test_filter_aligned_single_end -c ./tests/config/nextflow.config -stub
   tags:
-    - samtools/filter_aligned
+    - samtools/filteraligned
     - samtools
   files:
     - path: output/bwa/test.bam
     - path: output/bwa/test.bam.bai
     - path: output/bwa/versions.yml
-    - path: output/filter/test.unaligned.bam
-    - path: output/filter/versions.yml
+    - path: output/samtools/test.unaligned.bam
+    - path: output/samtools/versions.yml

tests/modules/CCBR/samtools/filter_aligned/custom_test.py → tests/modules/CCBR/samtools/filteraligned/test_filter_aligned.py

@@ -6,7 +6,7 @@
 @pytest.mark.workflow("samtools filter_aligned test_filter_aligned_paired_end")
 def test_unaligned_paired(workflow_dir):
     unaligned_bam_file = pysam.AlignmentFile(
-        pathlib.Path(workflow_dir, "output/filter/test.unaligned.bam"), "rb"
+        pathlib.Path(workflow_dir, "output/samtools/test.unaligned.bam"), "rb"
     )
     reads_are_good = list()
     for read in unaligned_bam_file:
@@ -19,7 +19,7 @@ def test_unaligned_paired(workflow_dir):
 @pytest.mark.workflow("samtools filter_aligned test_filter_aligned_single_end")
 def test_unaligned_single(workflow_dir):
     unaligned_bam_file = pysam.AlignmentFile(
-        pathlib.Path(workflow_dir, "output/filter/test.unaligned.bam"), "rb"
+        pathlib.Path(workflow_dir, "output/samtools/test.unaligned.bam"), "rb"
     )
     reads_are_good = list()
     for read in unaligned_bam_file: