fixed linting errors

software/bowtie/align/functions.nf

@@ -1,3 +1,4 @@
+
 /*
  * -----------------------------------------------------
  *  Utility functions used in nf-core DSL2 module files
@@ -56,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bowtie/index/functions.nf

@@ -1,3 +1,4 @@
+
 /*
  * -----------------------------------------------------
  *  Utility functions used in nf-core DSL2 module files
@@ -56,4 +57,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bowtie/index/meta.yml

@@ -7,45 +7,45 @@ keywords:
     - 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
+          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 `$params.outdir/<SOFTWARE>`
+          type: string
+          description: |
+              The pipeline's output directory. By default, the module will
+              output files into `$params.outdir/<SOFTWARE>`
     - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
+          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
+          type: boolean
+          description: |
+              Run the module with Conda using the software specified
+              via the `conda` directive
     - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.        
+          type: boolean
+          description: |
+              Instead of directly downloading Singularity images for use with Singularity,
+              force the workflow to pull and convert Docker containers instead.
 input:
     - fasta:
-        type: file
-        description: Input genome fasta file
+          type: file
+          description: Input genome fasta file
 output:
     - index:
-        type: file
-        description: Bowtie genome index files
-        pattern: "*.ebwt"
+          type: file
+          description: Bowtie genome index files
+          pattern: "*.ebwt"
     - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
 authors:
     - "@kevinmenden"

tests/software/bowtie/test.yml

@@ -17,7 +17,7 @@
     - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
 
-- name: Run bowtie index and align signle-end
+- name: Run bowtie index 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
@@ -40,8 +40,7 @@
     - path: output/bowtie/test.bam
       md5sum: 8179c68a819accbc9137dc881736106f
 
-
-- name: Run bowtie index and align paired_end
+- name: Run bowtie index and align paired-end
   command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - bowtie
@@ -63,4 +62,3 @@
       md5sum: a23e9a2a76e949aeb3693bcfae41a615
     - path: output/bowtie/test.bam
       md5sum: 9ce5aebf37128f4bb1d24e9548e22009
-