From 39897b6293354657fb86dc48f3aa45f9e7126cc6 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 11:14:20 +0100 Subject: [PATCH 01/16] update environment.yml --- environment.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/environment.yml b/environment.yml index 4d4851d98f..f8287ff1ec 100644 --- a/environment.yml +++ b/environment.yml @@ -6,28 +6,28 @@ channels: - bioconda - defaults dependencies: - - conda-forge::markdown=3.1.1 + - conda-forge::markdown=3.2.1 - conda-forge::pymdown-extensions=6.0 - conda-forge::pygments=2.5.2 - bioconda::ascat=2.5.2 - - bioconda::bcftools=1.9 + - bioconda::bcftools=1.10.2 - 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::htslib=1.10.2 + - bioconda::manta=1.6.0 - bioconda::multiqc=1.8 - - bioconda::qualimap=2.2.2b - - bioconda::samtools=1.9 + - bioconda::qualimap=2.2.2d + - bioconda::samtools=1.10 - bioconda::snpeff=4.3.1t - bioconda::strelka=2.9.10 - - bioconda::tiddit=2.7.1 + - bioconda::tiddit=2.10.0 - 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 \ No newline at end of file From c24c49c2d818dfa3a21dbf6c3cdb500d4ee3a642 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 11:22:55 +0100 Subject: [PATCH 02/16] add single_end params and set it to false to remove lint warning --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 7a44b22844..1ea5dd160a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -33,6 +33,7 @@ params { trim_nextseq = 0 save_trimmed = false split_fastq = null // Fastq files will not be split by default + single_end = false // No single end // Preprocessing markdup_java_options = '"-Xms4000m -Xmx7g"' // Established values for markDuplicate memory consumption, see https://github.com/SciLifeLab/Sarek/pull/689 for details @@ -50,7 +51,6 @@ params { pon_index = false // No default PON index for GATK Mutect2 / Sentieon TNscope target_bed = false // No default TargetBED file for targeted sequencing - // Annotation annotate_tools = null // Only with --step annotate annotation_cache = null // Annotation cache disabled From 8c07afa5c3556ae4a09d9926cb41dcc52252054a Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 11:30:40 +0100 Subject: [PATCH 03/16] spacing --- docs/usage.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index c06a875743..653787c914 100644 --- a/docs/usage.md +++ b/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) From aeb25476d266b32bae6f5b2af7bd5945260af452 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 11:31:25 +0100 Subject: [PATCH 04/16] fix link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5fefc7d0df..e827d9f329 100644 --- a/README.md +++ b/README.md @@ -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) From a4a9a89c1b0ef8c57a6873b27c0f2fc5ef3375fd Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 11:31:44 +0100 Subject: [PATCH 05/16] fix link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e827d9f329..4276c02dcc 100644 --- a/README.md +++ b/README.md @@ -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: From 8e8fa07d489ab5a8c678fb11faaff6ece1043233 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 11:40:16 +0100 Subject: [PATCH 06/16] remove link to figure --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4276c02dcc..8c73bcd706 100644 --- a/README.md +++ b/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.

- +

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). From 0d7948e369b881e301decd3f667252c5e351dfa2 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 13:10:54 +0100 Subject: [PATCH 07/16] update snpeff container --- containers/snpeff/Dockerfile | 11 ++++++++--- containers/snpeff/environment.yml | 2 +- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/containers/snpeff/Dockerfile b/containers/snpeff/Dockerfile index d08854d769..53ecdaf56f 100644 --- a/containers/snpeff/Dockerfile +++ b/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="maxime.garcia@scilifelab.se" +# 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 diff --git a/containers/snpeff/environment.yml b/containers/snpeff/environment.yml index e9b1f01e03..82ac3fe4f8 100644 --- a/containers/snpeff/environment.yml +++ b/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 From 004f260f2f8cd5d674c1cf503ac7b582acee1062 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 13:14:53 +0100 Subject: [PATCH 08/16] fix URLs --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b2fc20aeeb..e63c56cd47 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -318,7 +318,7 @@ 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 +327,7 @@ 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` From fd4426d5837567ac30a6e57f489c01cc5c4eb839 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 14:04:09 +0100 Subject: [PATCH 09/16] update vep containers + docs --- containers/vep/Dockerfile | 12 ++++++++---- containers/vep/environment.yml | 4 ++-- docs/containers.md | 34 ++++++++++++++++++---------------- 3 files changed, 28 insertions(+), 22 deletions(-) diff --git a/containers/vep/Dockerfile b/containers/vep/Dockerfile index 695e5ef865..4bf89db555 100644 --- a/containers/vep/Dockerfile +++ b/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="maxime.garcia@scilifelab.se" +# 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 \ diff --git a/containers/vep/environment.yml b/containers/vep/environment.yml index d44a829ed8..a357210e74 100644 --- a/containers/vep/environment.yml +++ b/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 diff --git a/docs/containers.md b/docs/containers.md index ddf6de64e8..e4bf4a3134 100644 --- a/docs/containers.md +++ b/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 **[BCFTools](https://github.com/samtools/bcftools)** 1.10.2 - 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 **[samtools](https://github.com/samtools/samtools)** 1.9 +- Contain **[HTSlib](https://github.com/samtools/htslib)** 1.10.2 +- 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)** 1.10 - 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 **[TIDDIT](https://github.com/SciLifeLab/TIDDIT)** 2.10.0 +- 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 From e1da70a180cbf58445f3533ebd6a7aebe9d5a362 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 15:57:46 +0100 Subject: [PATCH 10/16] refactor ASCAT --- main.nf | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/main.nf b/main.nf index 708b2cce92..6f060d2a69 100644 --- a/main.nf +++ b/main.nf @@ -69,8 +69,8 @@ def helpMessage() { --vep_cache [file] Specity the path to VEP cache, to be used with --annotation_cache --pon [file] Panel-of-normals VCF (bgzipped, indexed). See: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_CreateSomaticPanelOfNormals.php --pon_index [file] Index of pon panel-of-normals VCF - --ascat_ploidy [bool] Use this parameter together with to overwrite default behavior from ASCAT regarding ploidy. Note: Also requires that --ascat_purity is set. - --ascat_purity [bool] Use this parameter to overwrite default behavior from ASCAT regarding purity. Note: Also requires that --ascat_ploidy is set. + --ascat_ploidy [int] Use this parameter together with to overwrite default behavior from ASCAT regarding ploidy. Note: Also requires that --ascat_purity is set. + --ascat_purity [int] Use this parameter to overwrite default behavior from ASCAT regarding purity. Note: Also requires that --ascat_ploidy is set. Trimming: --trim_fastq [bool] Run Trim Galore @@ -2687,20 +2687,20 @@ process Ascat { script: gender = genderMap[idPatient] - ascat_purity=params.ascat_purity - ascat_ploidy=params.ascat_ploidy - if (params.ascat_purity && params.ascat_ploidy) + purity_ploidy = (params.ascat_purity && params.ascat_ploidy) ? "--purity ${params.ascat_purity} --ploidy ${params.ascat_ploidy}" : "" + """ + for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done + Rscript ${workflow.projectDir}/bin/run_ascat.r \ + --tumorbaf ${bafTumor} \ + --tumorlogr ${logrTumor} \ + --normalbaf ${bafNormal} \ + --normallogr ${logrNormal} \ + --tumorname ${idSampleTumor} \ + --basedir ${baseDir} \ + --gcfile ${acLociGC} \ + --gender ${gender} \ + ${purity_ploidy} """ - for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done - Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} --purity ${ascat_purity} --ploidy ${ascat_ploidy} - """ - else - """ - for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done - Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} - """ - - } ascatOut.dump(tag:'ASCAT') From fe1720a2e465194020c2f0c6839d8cbfd53b37a4 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 16:04:23 +0100 Subject: [PATCH 11/16] update vep download script --- downloadcache.nf | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/downloadcache.nf b/downloadcache.nf index 1a1048a7e8..f48ed2e34f 100644 --- a/downloadcache.nf +++ b/downloadcache.nf @@ -20,11 +20,11 @@ Usage: you're reading it DOWNLOAD CACHE: - nextflow run build.nf --download_cache [--snpEff_cache ] [--vep_cache ] + nextflow run build.nf --download_cache [--snpeff_cache ] [--vep_cache ] [--cadd_cache --cadd_version ] --download_cache Will download specified cache - --snpEff_cache + --snpeff_cache 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() @@ -152,7 +152,7 @@ ${summary.collect { k,v -> "
$k
${v ?: ' Date: Thu, 27 Feb 2020 17:24:49 +0100 Subject: [PATCH 12/16] keep 1.9 version of bcftools, htslib and samtools due to incompatibility issues --- docs/containers.md | 6 +++--- environment.yml | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/containers.md b/docs/containers.md index e4bf4a3134..0ea7963bb4 100644 --- a/docs/containers.md +++ b/docs/containers.md @@ -16,18 +16,18 @@ For annotation, the main container can be used, but the cache has to be download - 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)** 1.10.2 +- 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)** 11.5 - 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)** 1.10.2 +- Contain **[HTSlib](https://github.com/samtools/htslib)** 1.9 - 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)** 1.10 +- 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)** 2.10.0 diff --git a/environment.yml b/environment.yml index f8287ff1ec..2b658686bc 100644 --- a/environment.yml +++ b/environment.yml @@ -6,11 +6,11 @@ channels: - bioconda - defaults dependencies: - - conda-forge::markdown=3.2.1 + - conda-forge::markdown=3.1.1 - conda-forge::pymdown-extensions=6.0 - conda-forge::pygments=2.5.2 - bioconda::ascat=2.5.2 - - bioconda::bcftools=1.10.2 + - bioconda::bcftools=1.9 - bioconda::bwa=0.7.17 - bioconda::cancerit-allelecount=4.0.2 - bioconda::control-freec=11.5 @@ -19,11 +19,11 @@ dependencies: - bioconda::freebayes=1.3.2 - bioconda::gatk4-spark=4.1.4.1 - bioconda::genesplicer=1.0 - - bioconda::htslib=1.10.2 + - bioconda::htslib=1.9 - bioconda::manta=1.6.0 - bioconda::multiqc=1.8 - bioconda::qualimap=2.2.2d - - bioconda::samtools=1.10 + - bioconda::samtools=1.9 - bioconda::snpeff=4.3.1t - bioconda::strelka=2.9.10 - bioconda::tiddit=2.10.0 From 57c84c50b1dbf556e08652ebb29f111d7e7406ed Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 27 Feb 2020 17:27:12 +0100 Subject: [PATCH 13/16] keep tiddit 2.7.1 because recipe is still broken on bioconda --- docs/containers.md | 2 +- environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/containers.md b/docs/containers.md index 0ea7963bb4..01ba9476f3 100644 --- a/docs/containers.md +++ b/docs/containers.md @@ -30,7 +30,7 @@ For annotation, the main container can be used, but the cache has to be download - 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)** 2.10.0 +- Contain **[TIDDIT](https://github.com/SciLifeLab/TIDDIT)** 2.7.1 - 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 diff --git a/environment.yml b/environment.yml index 2b658686bc..dc427c9861 100644 --- a/environment.yml +++ b/environment.yml @@ -26,7 +26,7 @@ dependencies: - bioconda::samtools=1.9 - bioconda::snpeff=4.3.1t - bioconda::strelka=2.9.10 - - bioconda::tiddit=2.10.0 + - bioconda::tiddit=2.7.1 - bioconda::trim-galore=0.6.5 - bioconda::vcfanno=0.3.2 - bioconda::vcftools=0.1.16 From a6d82b5dae5274f2d74c9afc9c4a9c90b0763c8b Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 28 Feb 2020 08:33:14 +0100 Subject: [PATCH 14/16] handle fastq and fq files but give out warning --- main.nf | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 6f060d2a69..50e32d76b8 100644 --- a/main.nf +++ b/main.nf @@ -352,7 +352,7 @@ annotateTools = params.annotate_tools ? params.annotate_tools.split(',').collect if (!checkParameterList(annotateTools,annoList)) exit 1, 'Unknown tool(s) to annotate, see --help for more information' // Check parameters -if ((params.ascat_ploidy && !params.ascat_purity) || (!params.ascat_ploidy && params.ascat_purity)) exit 1, 'Please specify both ascat_purity and ascat_ploidy, or none of them' +if ((params.ascat_ploidy && !params.ascat_purity) || (!params.ascat_ploidy && params.ascat_purity)) exit 1, 'Please specify both --ascat_purity and --ascat_ploidy, or none of them' // Has the run name been specified by the user? // This has the bonus effect of catching both -name and --name @@ -3667,10 +3667,13 @@ def extractFastq(tsvFile) { def idRun = row[4] def file1 = returnFile(row[5]) def file2 = "null" - if (hasExtension(file1, "fastq.gz") || hasExtension(file1, "fq.gz")) { + if (hasExtension(file1, "fastq.gz") || hasExtension(file1, "fq.gz") || hasExtension(file1, "fastq") || hasExtension(file1, "fq")) { checkNumberOfItem(row, 7) file2 = returnFile(row[6]) - if (!hasExtension(file2, "fastq.gz") && !hasExtension(file2, "fq.gz")) exit 1, "File: ${file2} has the wrong extension. See --help for more information" + if (!hasExtension(file2, "fastq.gz") && !hasExtension(file2, "fq.gz") && !hasExtension(file2, "fastq") && !hasExtension(file2, "fq")) exit 1, "File: ${file2} has the wrong extension. See --help for more information" + if (hasExtension(file1, "fastq") || hasExtension(file1, "fq") || hasExtension(file2, "fastq") || hasExtension(file2, "fq")) { + log.warn "We do recommend to use gziped fastq file to help you reduce your data footprint." + } } else if (hasExtension(file1, "bam")) checkNumberOfItem(row, 6) else "No recognisable extention for input file: ${file1}" From ab2b516e651fad25984bf98f95f4ca70953db859 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 28 Feb 2020 08:43:59 +0100 Subject: [PATCH 15/16] update CHANGELOG --- CHANGELOG.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e63c56cd47..3cb97d37a4 100644 --- a/CHANGELOG.md +++ b/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` From bd6efdf36a17bddc95ad980139147ff8b055bb86 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 28 Feb 2020 08:56:27 +0100 Subject: [PATCH 16/16] exit instead of warning --- main.nf | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/main.nf b/main.nf index 50e32d76b8..b43da5d822 100644 --- a/main.nf +++ b/main.nf @@ -571,10 +571,10 @@ Channel.from(summary.collect{ [it.key, it.value] }) .map { k,v -> "
$k
${v ?: 'N/A'}
" } .reduce { a, b -> return [a, b].join("\n ") } .map { x -> """ - id: '{{ cookiecutter.name_noslash }}-summary' + id: 'sarek-summary' description: " - this information is collected when the pipeline is started." - section_name: '{{ cookiecutter.name }} Workflow Summary' - section_href: 'https://github.com/{{ cookiecutter.name }}' + section_name: 'nf-core/sarek Workflow Summary' + section_href: 'https://github.com/nf-core/sarek' plot_type: 'html' data: |
@@ -3323,9 +3323,9 @@ process Output_documentation { workflow.onComplete { // Set up the e-mail variables - def subject = "[{{ cookiecutter.name }}] Successful: $workflow.runName" + def subject = "[nf-core/sarek] Successful: $workflow.runName" if (!workflow.success) { - subject = "[{{ cookiecutter.name }}] FAILED: $workflow.runName" + subject = "[nf-core/sarek] FAILED: $workflow.runName" } def email_fields = [:] email_fields['version'] = workflow.manifest.version @@ -3355,12 +3355,12 @@ workflow.onComplete { if (workflow.success) { mqc_report = ch_multiqc_report.getVal() if (mqc_report.getClass() == ArrayList) { - log.warn "[{{ cookiecutter.name }}] Found multiple reports from process 'multiqc', will use only one" + log.warn "[nf-core/sarek] Found multiple reports from process 'multiqc', will use only one" mqc_report = mqc_report[0] } } } catch (all) { - log.warn "[{{ cookiecutter.name }}] Could not attach MultiQC report to summary email" + log.warn "[nf-core/sarek] Could not attach MultiQC report to summary email" } // Check if we are only sending emails on failure @@ -3392,11 +3392,11 @@ workflow.onComplete { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "[{{ cookiecutter.name }}] Sent summary e-mail to $email_address (sendmail)" + log.info "[nf-core/sarek] Sent summary e-mail to $email_address (sendmail)" } catch (all) { // Catch failures and try with plaintext [ 'mail', '-s', subject, email_address ].execute() << email_txt - log.info "[{{ cookiecutter.name }}] Sent summary e-mail to $email_address (mail)" + log.info "[nf-core/sarek] Sent summary e-mail to $email_address (mail)" } } @@ -3422,10 +3422,10 @@ workflow.onComplete { } if (workflow.success) { - log.info "-${c_purple}[{{ cookiecutter.name }}]${c_green} Pipeline completed successfully${c_reset}-" + log.info "-${c_purple}[nf-core/sarek]${c_green} Pipeline completed successfully${c_reset}-" } else { checkHostname() - log.info "-${c_purple}[{{ cookiecutter.name }}]${c_red} Pipeline completed with errors${c_reset}-" + log.info "-${c_purple}[nf-core/sarek]${c_red} Pipeline completed with errors${c_reset}-" } } @@ -3672,7 +3672,7 @@ def extractFastq(tsvFile) { file2 = returnFile(row[6]) if (!hasExtension(file2, "fastq.gz") && !hasExtension(file2, "fq.gz") && !hasExtension(file2, "fastq") && !hasExtension(file2, "fq")) exit 1, "File: ${file2} has the wrong extension. See --help for more information" if (hasExtension(file1, "fastq") || hasExtension(file1, "fq") || hasExtension(file2, "fastq") || hasExtension(file2, "fq")) { - log.warn "We do recommend to use gziped fastq file to help you reduce your data footprint." + exit 1, "We do recommend to use gziped fastq file to help you reduce your data footprint." } } else if (hasExtension(file1, "bam")) checkNumberOfItem(row, 6)