From ebbf0d5c08a1316f8d03897cfac48ea328219f14 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 6 Jul 2020 18:50:28 +0200
Subject: [PATCH] [Fix] bug in --fasta parameter
---
.github/workflows/ci.yml | 2 +-
CHANGELOG.md | 7 +++++++
Dockerfile | 4 ++--
environment.yml | 2 +-
main.nf | 6 +++---
nextflow.config | 4 ++--
6 files changed, 16 insertions(+), 9 deletions(-)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a7f734d..da1d4b7 100644
--- a/.github/workflows/ci.yml
+++ b/.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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6852128..e0ef895 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,13 @@
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`
diff --git a/Dockerfile b/Dockerfile
index 5aecaa6..7d67f49 100644
--- a/Dockerfile
+++ b/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
diff --git a/environment.yml b/environment.yml
index b9e6c02..e8944c6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,6 +1,6 @@
# 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
diff --git a/main.nf b/main.nf
index 7eb4315..10a1b95 100644
--- a/main.nf
+++ b/main.nf
@@ -182,8 +182,9 @@ if ( params.bwt2_index ){
}
else if ( params.fasta ) {
lastPath = params.fasta.lastIndexOf(File.separator)
- bwt2_base = params.fasta.substring(lastPath+1)
-
+ 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}
diff --git a/nextflow.config b/nextflow.config
index f7a5af7..391610d 100644
--- a/nextflow.config
+++ b/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
--
GitLab