From 06bc08eaaa34994269e4881399e2ca4e944c9226 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Tue, 30 Apr 2019 14:57:40 +0200
Subject: [PATCH] fix conda env
---
environment.yml | 6 +++---
main.nf | 4 +++-
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/environment.yml b/environment.yml
index ed47c8b..745fdbc 100644
--- a/environment.yml
+++ b/environment.yml
@@ -6,7 +6,7 @@ channels:
- bioconda
- defaults
dependencies:
- - python=2.7.13
+ - python=2.7.16
- pip=18.1
- conda-forge::scipy=1.0.1
- conda-forge::numpy=1.9.3
@@ -15,7 +15,7 @@ dependencies:
- bioconda::pysam=0.14.1
- cooler=0.8.3
- bowtie2=2.3.5
- - samtools=1.7
- - multiqc=1.6
+ - samtools=1.9
+ - bioconda::multiqc=1.7
- pip:
- iced==0.4.2
diff --git a/main.nf b/main.nf
index 17ff4d3..eeb6923 100644
--- a/main.nf
+++ b/main.nf
@@ -236,6 +236,7 @@ summary['Run Name'] = custom_runName ?: workflow.runName
summary['Reads'] = params.reads
summary['splitFastq'] = params.splitFastq
summary['Fasta Ref'] = params.fasta
+summary['Restriction Motif']= params.restriction_site
summary['Ligation Motif'] = params.ligation_site
summary['DNase Mode'] = params.dnase
summary['Remove Dup'] = params.rm_dup
@@ -311,8 +312,9 @@ process get_software_versions {
echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
bowtie2 --version > v_bowtie2.txt
- python --version > v_python.txt
+ python --version > v_python.txt 2>&1
samtools --version > v_samtools.txt
+ multiqc --version > v_multiqc.txt
scrape_software_versions.py &> software_versions_mqc.yaml
"""
}
--
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