update dependencies and prepare v1.1

Dockerfile

@@ -1,22 +1,23 @@
-################## BASE IMAGE ######################
-FROM nfcore/base
+################## BASE IMAGE #####################
+FROM continuumio/miniconda3:4.7.12
 
-################## METADATA ######################
+################## METADATA #######################
 
-LABEL base_image="nfcore/base"
-LABEL version="1.0"
-LABEL software="FastQC-nf"
-LABEL software.version="1.0"
-LABEL about.summary="Container image containing all requirements for FastQC-nf"
-LABEL about.home="http://github.com/IARCbioinfo/FastQC-nf"
-LABEL about.documentation="http://github.com/IARCbioinfo/FastQC-nf/README.md"
-LABEL about.license_file="http://github.com/IARCbioinfo/FastQC-nf/LICENSE.txt"
+LABEL base_image="continuumio/miniconda3"
+LABEL version="4.7.12"
+LABEL software="fastqc-nf"
+LABEL software.version="1.1"
+LABEL about.summary="Container image containing all requirements for fastqc-nf"
+LABEL about.home="http://github.com/IARCbioinfo/fastqc-nf"
+LABEL about.documentation="http://github.com/IARCbioinfo/fastqc-nf/README.md"
+LABEL about.license_file="http://github.com/IARCbioinfo/fastqc-nf/LICENSE.txt"
 LABEL about.license="GNU-3.0"
 
 ################## MAINTAINER ######################
-MAINTAINER Tiffany Delhomme <delhommet@students.iarc.fr>
+MAINTAINER **nalcala** <**alcalan@iarc.fr**>
 
 ################## INSTALLATION ######################
-
 COPY environment.yml /
-RUN conda env update -n root -f /environment.yml && conda clean -a
+RUN apt-get update && apt-get install -y procps && apt-get clean -y
+RUN conda env create -n fastqc-nf -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/fastqc-nf/bin:$PATH

FastQC.nf

@@ -25,9 +25,9 @@ params.cpu = 2
 params.mem = 10
 
 log.info ""
-log.info "----------------------------------------------------------------"
-log.info "    Unaligned reads quality control with FastQC and MultiQC     "
-log.info "----------------------------------------------------------------"
+log.info "-----------------------------------------------------------------------"
+log.info "fastqc-nf v1.1: Unaligned reads quality control with FastQC and MultiQC"
+log.info "-----------------------------------------------------------------------"
 log.info "Copyright (C) IARC/WHO"
 log.info "This program comes with ABSOLUTELY NO WARRANTY; for details see LICENSE"
 log.info "This is free software, and you are welcome to redistribute it"
@@ -38,13 +38,11 @@ if (params.help) {
     log.info "                     USAGE                              "
     log.info "--------------------------------------------------------"
     log.info ""
-    log.info "----------nextflow pipeline for QC on fastq files-------"
-    log.info ""
-    log.info "nextflow run FastQC.nf --input_folder path/to/fastq/ --fastqc path/to/fastqc/ --multiqc path/to/multiqc/  --output_folder /path/to/output"
+    log.info "nextflow run IARCbioinfo/fastqc-nf --input_folder path/to/fastq/ --output_folder /path/to/output [OPTIONS]"
     log.info ""
     log.info "Mandatory arguments:"
     log.info "--input_folder         FOLDER               Folder containing fastq files"
-    log.info "--output_folder        PATH                 Output directory for html and zip files (default=fastqc_ouptut)"
+    log.info "--output_folder        FOLDER                 Output directory for html and zip files (default=fastqc_ouptut)"
     log.info ""
     log.info "Optional arguments:"
     log.info '--ext                  STRING               Extension of files (default : fastq.gz)'

Singularity/Singularity.v1.1

@@ -0,0 +1,7 @@
+From:iarcbioinfo/fastqc-nf:v1.1
+Bootstrap:docker
+
+%labels
+    MAINTAINER **alcalan** <**[email protected]**>
+    DESCRIPTION Container image containing all requirements for pipeline fastqc-nf
+    VERSION 1.1

environment.yml

@@ -3,8 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - defaults
-channel_priority: strict
 dependencies:
-  - fastqc=0.11.8
-  - multiqc=1.7
-  - samtools=1.9
+  - fastqc=0.11.9
+  - multiqc=1.9
+  - samtools=1.10

nextflow.config

@@ -9,16 +9,19 @@ process {
     shell =  ['/bin/bash','-o','pipefail']
 }
 
-
 profiles {
-  conda { process.conda = "$baseDir/environment.yml" }
+  conda { 
+	process.conda = "$baseDir/environment.yml"
+	conda.createTimeout = "200 min"
+	}
   docker {
-    docker.enabled = true
-    process.container = 'iarcbioinfo/fastqc-nf'
+    docker.enabled = true 
+    process.container = 'iarcbioinfo/fastqc-nf:v1.1'
   }
   singularity {
-    singularity.enabled = true
-    process.container = 'iarcbioinfo/fastqc-nf'
+    singularity.enabled = true 
+    process.container = 'shub://IARCbioinfo/fastqc-nf:v1.1'
+    pullTimeout = "200 min"
   }
 }