Add tests for subread #106 (#393)

* inital commit

* added meta.yaml info

* add initial logic for featurecounts test

* add args and change SE/PE to strandedness for featurecounts test

* added tests to pytest

* added test.yml

* removed GTF flag in options

* corrected test meta params

* meta yaml corrected tool info

* update test.yml

* fix lint errors meta.yml

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>

software/subread/featurecounts/meta.yml

@@ -0,0 +1,52 @@
+name: subread_featurecounts
+description: Count reads that map to genomic features
+keywords:
+    - counts
+    - fasta
+    - genome
+    - reference
+
+tools:
+  - featurecounts:
+      description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
+      homepage: http://bioinf.wehi.edu.au/featureCounts/
+      documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
+      doi: "10.1093/bioinformatics/btt656"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/SAM file containing read alignments
+      pattern: "*.{bam}"
+  - annotation:
+      type: file
+      description: Genomic features annotation in GTF or SAF
+      pattern: "*.{gtf,saf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+  - counts:
+      type: file
+      description: Counts of reads mapping to features
+      pattern: "*featureCounts.txt"
+  - summary:
+      type: file
+      description: Summary log file
+      pattern: "*.featureCounts.txt.summary"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@ntoda03"

tests/config/pytest_software.yml

@@ -466,6 +466,10 @@ stringtie:
   - software/stringtie/**
   - tests/software/stringtie/**
 
+subread_featurecounts:
+  - software/subread/featurecounts/**
+  - tests/software/subread/featurecounts/**
+
 tabix_bgzip:
   - software/tabix/bgzip/**
   - tests/software/tabix/bgzip/**

tests/software/subread/featurecounts/main.nf

@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SUBREAD_FEATURECOUNTS } from '../../../../software/subread/featurecounts/main.nf' addParams( options: [args:'-t CDS'] )
+
+workflow test_subread_featurecounts_forward {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}
+
+workflow test_subread_featurecounts_reverse {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}
+
+workflow test_subread_featurecounts_unstranded {
+    
+    def input = []
+    input = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
+
+    SUBREAD_FEATURECOUNTS ( input )
+}

tests/software/subread/featurecounts/test.yml

@@ -0,0 +1,35 @@
+- name: subread featurecounts test_subread_featurecounts_forward
+  command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_forward -c tests/config/nextflow.config
+  tags:
+    - subread
+    - subread_featurecounts_forward
+    - subread_featurecounts
+  files:
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: d78617192451a57f6ef249ddcaf13720
+    - path: output/subread/test.featureCounts.txt
+      md5sum: b0a1f7563afe49007f422d4c9ca5ee6c
+
+- name: subread featurecounts test_subread_featurecounts_reverse
+  command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config
+  tags:
+    - subread
+    - subread_featurecounts
+    - subread_featurecounts_reverse
+  files:
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: 4217004d0b55f870f77092364f59e44d
+    - path: output/subread/test.featureCounts.txt
+      md5sum: 412840a8880cd29674b3d5404d3de19b
+
+- name: subread featurecounts test_subread_featurecounts_unstranded
+  command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config
+  tags:
+    - subread
+    - subread_featurecounts
+    - subread_featurecounts_unstranded
+  files:
+    - path: output/subread/test.featureCounts.txt.summary
+      md5sum: ee585faeb1edfcd2188a5e486a0e98a9
+    - path: output/subread/test.featureCounts.txt
+      md5sum: 6b684e11a1e54bec7e1ee5e3f651d7fd