Merge pull request #132 from drpatelh/bowtie

Rename bowtie_index to bowtie_build

.github/workflows/bowtie_build.yml

@@ -1,14 +1,14 @@
-name: bowtie_index
+name: bowtie_build
 on:
   push:
     paths:
-      - software/bowtie/index/**
-      - .github/workflows/bowtie_index.yml
+      - software/bowtie/build/**
+      - .github/workflows/bowtie_build.yml
       - tests/software/bowtie/**
   pull_request:
     paths:
-      - software/bowtie/index/**
-      - .github/workflows/bowtie_index.yml
+      - software/bowtie/build/**
+      - .github/workflows/bowtie_build.yml
       - tests/software/bowtie/**
 
 jobs:
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bowtie_index --symlink --wt 2
+      - run: pytest --tag bowtie_build --symlink --wt 2

software/bowtie/build/main.nf

@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 def options    = initOptions(params.options)
 
-process BOWTIE_INDEX {
+process BOWTIE_BUILD {
     tag "$fasta"
     label 'process_high'
     publishDir "${params.outdir}",
@@ -22,11 +22,11 @@ process BOWTIE_INDEX {
     path fasta
 
     output:
-    path 'bowtie', emit: index
+    path 'bowtie'       , emit: index
     path '*.version.txt', emit: version
 
     script:
-    def software  = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
     """
     mkdir bowtie
     bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}

software/bowtie/build/meta.yml

@@ -1,4 +1,4 @@
-name: bowtie_index
+name: bowtie_build
 description: Create bowtie index for reference genome
 keywords:
     - index
@@ -49,3 +49,4 @@ output:
           pattern: "*.{version.txt}"
 authors:
     - "@kevinmenden"
+    - "@drpatelh"

tests/software/bowtie/main.nf

@@ -2,32 +2,32 @@
 
 nextflow.enable.dsl = 2
 
-include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
+include { BOWTIE_BUILD } from '../../../software/bowtie/build/main.nf' addParams( options: [:] )
 include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf'  addParams( options: [:] )
 
-workflow test_bowtie_index {
+workflow test_bowtie_build {
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
-    BOWTIE_INDEX ( fasta ) 
+    BOWTIE_BUILD ( fasta )
 }
 
 workflow test_bowtie_alignment_single_end {
 
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
-    BOWTIE_INDEX ( fasta ) 
+    BOWTIE_BUILD ( fasta )
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
-    BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
 }
 
 workflow test_bowtie_alignment_paired_end {
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
-    BOWTIE_INDEX ( fasta ) 
+    BOWTIE_BUILD ( fasta )
 
     def input = []
     input = [ [ id:'test', single_end:false ], // meta map
               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
-    BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
+    BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
 }

tests/software/bowtie/test.yml

@@ -1,8 +1,8 @@
-- name: Run bowtie index
-  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
+- name: Run bowtie build
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config
   tags:
     - bowtie
-    - bowtie_index
+    - bowtie_build
   files:
     - path: output/bowtie/bowtie/NC_010473.1.ebwt
       md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
@@ -17,7 +17,7 @@
     - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
 
-- name: Run bowtie index and align single-end
+- name: Run bowtie build and align single-end
   command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
     - bowtie