Merge pull request #68 from nservant/dev

Bug with --fasta parameter

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Pull docker image
         run: |
           docker pull nfcore/hic:dev
-          docker tag nfcore/hic:dev nfcore/hic:1.2.0
+          docker tag nfcore/hic:dev nfcore/hic:1.2.1
       - name: Run pipeline with test data
         run: |
           # nf-core: You can customise CI pipeline run tests as required

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## v1.2.1 - 2020-07-06
+
+### `Fixed`
+
+* Fix issue with `--fasta` option and `.fa` extension (#66)
+
 ## v1.2.0 - 2020-06-18
 
 ### `Added`

Dockerfile

@@ -7,8 +7,8 @@ RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-hic-1.2.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.2.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-hic-1.2.0 > nf-core-hic-1.2.0.yml
+RUN conda env export --name nf-core-hic-1.2.1 > nf-core-hic-1.2.1.yml
 

environment.yml

 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-hic-1.2.0
+name: nf-core-hic-1.2.1
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -181,9 +181,10 @@ if ( params.bwt2_index ){
 
 }
 else if ( params.fasta ) {
-    lastPath = params.fasta.lastIndexOf(File.separator)
-    bwt2_base = params.fasta.substring(lastPath+1)
-
+   lastPath = params.fasta.lastIndexOf(File.separator)
+   fasta_base = params.fasta.substring(lastPath+1)
+   bwt2_base = fasta_base.toString() - ~/(\.fa)?(\.fasta)?(\.fas)?(\.fsa)?$/
+ 
    Channel.fromPath( params.fasta )
 	.ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
         .set { fasta_for_index }
@@ -361,7 +362,6 @@ if(!params.bwt2_index && params.fasta){
 	file "bowtie2_index" into bwt2_index_trim
 
         script:
-        bwt2_base = fasta.toString() - ~/(\.fa)?(\.fasta)?(\.fas)?$/
         """
         mkdir bowtie2_index
 	bowtie2-build ${fasta} bowtie2_index/${bwt2_base}

nextflow.config

@@ -64,7 +64,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/hic:1.2.0'
+process.container = 'nfcore/hic:1.2.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -135,7 +135,7 @@ manifest {
   description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.2.0'
+  version = '1.2.1'
 }
 
 // Function to ensure that resource requirements don't go beyond