added module yml files

software/bowtie/align/main.nf

@@ -17,7 +17,6 @@ process BOWTIE_ALIGN {
     input:
     tuple val(meta), path(reads)
     path  index
-    path  gtf
     
     output:
     tuple val(meta), path("*.sam")            , emit: sam

software/bowtie/align/meta.yml

@@ -0,0 +1,57 @@
+name: bowtie_align
+description: Align reads to a reference genome using bowtie
+keywords:
+    - align
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie:
+        description: |
+            bowtie is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bowtie-bio.sourceforge.net/index.shtml
+        documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+        arxiv: arXiv:1303.3997
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+            respectively.
+    - index:
+        type: file
+        description: Bowtie genome index files
+        pattern: "*.ebwt"
+output:
+    - index:
+        type: file
+        description: Bowtie genome index files
+        pattern: "*.ebwt"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@kevinmenden"

software/bowtie/index/main.nf

@@ -17,7 +17,6 @@ process BOWTIE_INDEX {
 
     input:
     path fasta
-    path gtf
 
     output:
     path "*.index*"          , emit: index

software/bowtie/index/meta.yml

@@ -0,0 +1,46 @@
+name: bowtie_index
+description: Create bowtie index for reference genome
+keywords:
+    - index
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie:
+        description: |
+            bowtie is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bowtie-bio.sourceforge.net/index.shtml
+        documentation: http://bowtie-bio.sourceforge.net/manual.shtml
+        arxiv: arXiv:1303.3997
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+input:
+    - fasta:
+        type: file
+        description: Input genome fasta file
+output:
+    - index:
+        type: file
+        description: Bowtie genome index files
+        pattern: "*.ebwt"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@kevinmenden"

tests/software/bowtie/main.nf

@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
+include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf'  addParams( options: [:] )
+
+
+
+workflow test_bowtie_index {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+}
+
+workflow test_bowtie_alignment_single_end {
+
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    BOWTIE_INDEX ( fasta ) 
+}
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
+    BOWTIE_ALIGN ( input, BOWTIE_INDEX.index )
+}
+

tests/software/bowtie/test.yml

@@ -0,0 +1,32 @@
+- name: Run bowtie index
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_index
+  files:
+    - path: output/bwa/NC_010473.fa.amb
+      md5sum: 942a990ae872f1c0b8d72dda2db405d5
+    - path: output/bwa/NC_010473.fa.bwt
+      md5sum: 7301b52e2ecb893d429a49fa692447ae
+    - path: output/bwa/NC_010473.fa.pac
+      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
+    - path: output/bwa/NC_010473.fa.sa
+      md5sum: a47dcc92e750e2f16fbd979b8ff9538e
+
+- name: Run bwa mem single-end
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+  files:
+    - path: output/test_single_end/test.bam
+      md5sum: 3ee21210bac387e0335008146e4728bc
+
+- name: Run bwa mem paired-end
+  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
+  tags:
+    - bwa
+    - bwa_mem
+  files:
+    - path: output/test_paired_end/test.bam
+      md5sum: 510d8acc6448c07cdacce8e64ec0904c