Merge pull request #131 from MaxUlysse/prepare2.6

Prepare for 2.6 release

CHANGELOG.md

@@ -8,10 +8,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 
 ### `Added`
 
-- [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
 - [#76](https://github.com/nf-core/sarek/pull/76) - Add `GATK Spark` possibilities to Sarek
 - [#87](https://github.com/nf-core/sarek/pull/87) - Add `GATK BaseRecalibrator` plot to `MultiQC` report
 - [#115](https://github.com/nf-core/sarek/pull/115) - Add [@szilvajuhos](https://github.com/szilvajuhos) abstract for ESHG2020
+- [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
 
 ### `Changed`
 
@@ -25,7 +25,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#113](https://github.com/nf-core/sarek/pull/113) - Move social preview image
 - [#120](https://github.com/nf-core/sarek/pull/120) - Sync TEMPLATE
 - [#121](https://github.com/nf-core/sarek/pull/121) - Update `MultiQC` to `1.8`
-- [#126](https://github.com/nf-core/sarek/pull/126) - Update docs
+- [#126](https://github.com/nf-core/sarek/pull/126), [#131](https://github.com/nf-core/sarek/pull/131) - Update docs
+- [#131](https://github.com/nf-core/sarek/pull/131) - Use `nfcore/base:1.9` as base for containers
+- [#131](https://github.com/nf-core/sarek/pull/131) - Update `Control-FREEC` to `11.5`
+- [#131](https://github.com/nf-core/sarek/pull/131) - Update `FastQC` to `0.11.9`
+- [#131](https://github.com/nf-core/sarek/pull/131) - Update `FreeBayes` to `1.3.2`
+- [#131](https://github.com/nf-core/sarek/pull/131) - Update `Manta` to `1.6.0`
+- [#131](https://github.com/nf-core/sarek/pull/131) - Update `Qualimap` to `2.2.2d`
+- [#131](https://github.com/nf-core/sarek/pull/131) - Update `VEP` to `99.2`
 
 ### `Fixed`
 
@@ -318,7 +325,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#728](https://github.com/SciLifeLab/Sarek/pull/728) - `Strelka` Best Practices output is now prefixed with `StrelkaBP_`
 - [#728](https://github.com/SciLifeLab/Sarek/pull/728) - VCFs and Annotated VCFs are now ordered by Patient, then tools
 - [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Merge `buildContainers.nf` and `buildReferences.nf` in `build.nf`
-- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Reduce number of CPUs for `RunVEP` to `4` cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html)
+- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Reduce number of CPUs for `RunVEP` to `4` cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#faster)
 - [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Update `VEP` from `95.1` to `95.2`
 
 ### `Removed`
@@ -327,7 +334,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#719](https://github.com/SciLifeLab/Sarek/pull/719) - `snpEff` base container is no longer used
 - [#721](https://github.com/SciLifeLab/Sarek/pull/721) - Remove `COSMIC` docs
 - [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Remove `defineDirectoryMap()`
-- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Remove `--database` option for VEP cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html)
+- [#732](https://github.com/SciLifeLab/Sarek/pull/732) - Remove `--database` option for VEP cf: [VEP docs](https://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#faster)
 
 ### `Fixed`
 

README.md

@@ -22,7 +22,7 @@ It's built using [Nextflow](https://www.nextflow.io), a workflow tool to run tas
 It comes with docker containers making installation trivial and results highly reproducible.
 
 <p align="center">
-    <a href="./docs/images/sarek_workflow.png"><img title="Sarek Workflow" src="./docs/images/sarek_workflow.png" width=40%></a>
+    <img title="Sarek Workflow" src="docs/images/sarek_workflow.png" width=40%>
 </p>
 
 It's listed on the [Elixir - Tools and Data Services Registry](https://bio.tools/Sarek), [Dockstore](https://dockstore.org/workflows/github.com/nf-core/sarek) and [omicX - Bioinformatics tools](https://omictools.com/sarek-tool).
@@ -73,7 +73,7 @@ The nf-core/sarek pipeline comes with documentation about the pipeline, found in
 
 ## Credits
 
-Sarek was developed at the [National Genomics Infastructure](https://ngisweden.scilifelab.se) and [National Bioinformatics Infastructure Sweden](https://nbis.se) which are both platforms at [SciLifeLab](https://scilifelab.se), with the support of [The Swedish Childhood Tumor Biobank (Barntumörbanken)](ttps://ki.se/forskning/barntumorbanken-0).
+Sarek was developed at the [National Genomics Infastructure](https://ngisweden.scilifelab.se) and [National Bioinformatics Infastructure Sweden](https://nbis.se) which are both platforms at [SciLifeLab](https://scilifelab.se), with the support of [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken).
 
 Main authors:
 
@@ -109,7 +109,7 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 
 ## Acknowledgements
 
-[![Barntumörbanken](docs/images/BTB_logo.png)](https://ki.se/forskning/barntumorbanken-0) | [![SciLifeLab](docs/images/SciLifeLab_logo.png)](https://scilifelab.se)
+[![Barntumörbanken](docs/images/BTB_logo.png)](https://ki.se/forskning/barntumorbanken) | [![SciLifeLab](docs/images/SciLifeLab_logo.png)](https://scilifelab.se)
 :-:|:-:
 [![National Genomics Infrastructure](docs/images/NGI_logo.png)](https://ngisweden.scilifelab.se/) | [![National Bioinformatics Infrastructure Sweden](docs/images/NBIS_logo.png)](https://nbis.se)
 

containers/snpeff/Dockerfile

@@ -1,13 +1,18 @@
-FROM nfcore/base:1.7
-
+FROM nfcore/base:1.9
 LABEL \
   author="Maxime Garcia" \
   description="snpEff image for use in nf-core/sarek" \
   maintainer="[email protected]"
 
+# Install the conda environment
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/sarek-snpeff-dev/bin:$PATH
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-sarek-snpeff-dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-sarek-snpeff-dev > nf-core-sarek-snpeff-dev.yml
 
 # Setup default ARG variables
 ARG GENOME=GRCh38

containers/snpeff/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: sarek-snpeff-dev
+name: nf-core-sarek-snpeff-dev
 channels:
   - conda-forge
   - bioconda

containers/vep/Dockerfile

@@ -1,13 +1,18 @@
-FROM nfcore/base:1.7
-
+FROM nfcore/base:1.9
 LABEL \
   author="Maxime Garcia" \
   description="VEP image for use in nf-core/sarek" \
   maintainer="[email protected]"
 
+# Install the conda environment
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/sarek-vep-dev/bin:$PATH
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-sarek-vep-dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-sarek-vep-dev > nf-core-sarek-vep-dev.yml
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
@@ -19,7 +24,6 @@ RUN vep_install \
   -a c \
   -c .vep \
   -s ${SPECIES} \
-  -v ${VEP_VERSION} \
   -y ${GENOME} \
   --CACHE_VERSION ${VEP_VERSION} \
   --CONVERT \

containers/vep/environment.yml

@@ -1,11 +1,11 @@
 # You can use this file to create a conda environment for this pipeline:
 # conda env create -f environment.yml
-name: sarek-vep-dev
+name: nf-core-sarek-vep-dev
 channels:
   - conda-forge
   - bioconda
   - defaults
 
 dependencies:
-  - ensembl-vep=95.2
+  - ensembl-vep=99.2
   - genesplicer=1.0

docs/containers.md

@@ -13,39 +13,41 @@ For annotation, the main container can be used, but the cache has to be download
 
 ### sarek [![sarek-docker status](https://img.shields.io/docker/automated/nfcore/sarek.svg)](https://hub.docker.com/r/nfcore/sarek)
 
-- Based on `nfcore/base:latest`
+- Based on `nfcore/base:1.9`
 - Contain **[ASCAT](https://github.com/Crick-CancerGenomics/ascat)** 2.5.2
 - Contain **[AlleleCount](https://github.com/cancerit/alleleCount)** 4.0.2
 - Contain **[BCFTools](https://github.com/samtools/bcftools)** 1.9
 - Contain **[BWA](https://github.com/lh3/bwa)** 0.7.17
-- Contain **[Control-FREEC](https://github.com/BoevaLab/FREEC)** 11.4
-- Contain **[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)** 0.11.8
-- Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.2.0
+- Contain **[Control-FREEC](https://github.com/BoevaLab/FREEC)** 11.5
+- Contain **[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)** 0.11.9
+- Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.3.2
 - Contain **[GATK4-spark](https://github.com/broadinstitute/gatk)** 4.1.4.1
 - Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0
 - Contain **[HTSlib](https://github.com/samtools/htslib)** 1.9
-- Contain **[Manta](https://github.com/Illumina/manta)** 1.5.0
-- Contain **[MultiQC](https://github.com/ewels/MultiQC/)** 1.7
-- Contain **[Qualimap](http://qualimap.bioinfo.cipf.es)** 2.2.2b
+- Contain **[Manta](https://github.com/Illumina/manta)** 1.6.0
+- Contain **[MultiQC](https://github.com/ewels/MultiQC/)** 1.8
+- Contain **[Qualimap](http://qualimap.bioinfo.cipf.es)** 2.2.2d
 - Contain **[samtools](https://github.com/samtools/samtools)** 1.9
 - Contain **[snpEff](http://snpeff.sourceforge.net/)** 4.3.1t
 - Contain **[Strelka2](https://github.com/Illumina/strelka)** 2.9.10
 - Contain **[TIDDIT](https://github.com/SciLifeLab/TIDDIT)** 2.7.1
-- Contain **[VCFanno](https://github.com/brentp/vcfanno)** 0.3.1
+- Contain **[pigz](https://zlib.net/pigz/)** 2.3.4
+- Contain **[Trim Galore](https://github.com/FelixKrueger/TrimGalore)** 0.6.5
+- Contain **[VCFanno](https://github.com/brentp/vcfanno)** 0.3.2
 - Contain **[VCFtools](https://vcftools.github.io/index.html)** 0.1.16
-- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 95.2
+- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 99.2
 
 ### sareksnpeff [![sareksnpeff-docker status](https://img.shields.io/docker/automated/nfcore/sareksnpeff.svg)](https://hub.docker.com/r/nfcore/sareksnpeff)
 
-- Based on `nfcore/base:latest`
+- Based on `nfcore/base:1.9`
 - Contain **[snpEff](http://snpeff.sourceforge.net/)** 4.3.1t
 - Contains cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1`
 
 ### sarekvep [![sarekvep-docker status](https://img.shields.io/docker/automated/nfcore/sarekvep.svg)](https://hub.docker.com/r/nfcore/sarekvep)
 
-- Based on `nfcore/base:latest`
+- Based on `nfcore/base:1.9`
 - Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0
-- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 95.2
+- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 99.2
 - Contain cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1`
 
 ## Building your own

docs/usage.md

@@ -84,8 +84,8 @@
   - [--awscli](#--awscli)
 - [Other command line parameters](#other-command-line-parameters)
   - [--outdir](#--outdir)
-- [--publish_dir_mode](#--publish_dir_mode)
-- [--publishDirMode](#--publishdirmode)
+  - [--publish_dir_mode](#--publish_dir_mode)
+  - [--publishDirMode](#--publishdirmode)
   - [--sequencing_center](#--sequencing_center)
   - [--email](#--email)
   - [--email_on_fail](#--email_on_fail)
@@ -799,13 +799,13 @@ Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a
 The output directory where the results will be saved.
 Default: `results/`
 
-## --publish_dir_mode
+### --publish_dir_mode
 
 The file publishing method.
 Available: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`
 Default: `copy`
 
-## --publishDirMode
+### --publishDirMode
 
 > :warning: This params is deprecated -- it will be removed in a future release.
 > Please check: [`--publish_dir_mode`](#--publish_dir_mode)

downloadcache.nf

@@ -20,11 +20,11 @@ Usage:
       you're reading it
 
 DOWNLOAD CACHE:
-  nextflow run build.nf --download_cache [--snpEff_cache <pathToSNPEFFcache>] [--vep_cache <pathToVEPcache>]
+  nextflow run build.nf --download_cache [--snpeff_cache <pathToSNPEFFcache>] [--vep_cache <pathToVEPcache>]
                                          [--cadd_cache <pathToCADDcache> --cadd_version <CADD Version>]
     --download_cache
       Will download specified cache
-    --snpEff_cache <Directoy>
+    --snpeff_cache <Directoy>
       Specify path to snpEff cache
       If none, will use snpEff version specified in configuration
       Will use snpEff cache version for ${params.genome}: ${params.genomes[params.genome].snpeffDb} in igenomes configuration file:
@@ -55,7 +55,7 @@ params.offline = null
 params.cadd_cache = null
 params.cadd_version = 'v1.5'
 params.genome = 'GRCh37'
-params.snpEff_cache = null
+params.snpeff_cache = null
 params.vep_cache = null
 
 ch_referencesFiles = Channel.empty()
@@ -152,15 +152,15 @@ ${summary.collect { k,v -> "            <dt>$k</dt><dd><samp>${v ?: '<span style
 process BuildCache_snpEff {
   tag {snpeffDb}
 
-  publishDir params.snpEff_cache, mode: params.publishDirMode
+  publishDir params.snpeff_cache, mode: params.publishDirMode
 
   input:
     val snpeffDb from Channel.value(params.genomes[params.genome].snpeffDb)
 
   output:
     file("*")
 
-  when: params.snpEff_cache && params.download_cache && !params.offline
+  when: params.snpeff_cache && params.download_cache && !params.offline
 
   script:
   """
@@ -189,7 +189,6 @@ process BuildCache_VEP {
     -a cf \
     -c . \
     -s ${species} \
-    -v ${cache_version} \
     -y ${genome} \
     --CACHE_VERSION ${cache_version} \
     --CONVERT \

environment.yml

@@ -13,21 +13,21 @@ dependencies:
   - bioconda::bcftools=1.9
   - bioconda::bwa=0.7.17
   - bioconda::cancerit-allelecount=4.0.2
-  - bioconda::control-freec=11.4
-  - bioconda::ensembl-vep=95.2
-  - bioconda::fastqc=0.11.8
-  - bioconda::freebayes=1.2.0
+  - bioconda::control-freec=11.5
+  - bioconda::ensembl-vep=99.2
+  - bioconda::fastqc=0.11.9
+  - bioconda::freebayes=1.3.2
   - bioconda::gatk4-spark=4.1.4.1
   - bioconda::genesplicer=1.0
   - bioconda::htslib=1.9
-  - bioconda::manta=1.5.0
+  - bioconda::manta=1.6.0
   - bioconda::multiqc=1.8
-  - bioconda::qualimap=2.2.2b
+  - bioconda::qualimap=2.2.2d
   - bioconda::samtools=1.9
   - bioconda::snpeff=4.3.1t
   - bioconda::strelka=2.9.10
   - bioconda::tiddit=2.7.1
   - bioconda::trim-galore=0.6.5
-  - bioconda::vcfanno=0.3.1
+  - bioconda::vcfanno=0.3.2
   - bioconda::vcftools=0.1.16
   - conda-forge::pigz=2.3.4