fix conda env

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

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
    """
 }