From 88079ed443aefd3816b4b7636121dee36bfda6ed Mon Sep 17 00:00:00 2001 From: Praveen Date: Tue, 17 May 2022 14:16:56 +0200 Subject: [PATCH 1/4] removed files_unchanged --- .nf-core.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index abfd2795..3805dc81 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1 @@ repository_type: pipeline -lint: - files_unchanged: - - assets/email_template.html From 7f15f58b298bf4c1bb0118f75841ebfdf64386dd Mon Sep 17 00:00:00 2001 From: Praveen Date: Tue, 17 May 2022 14:17:43 +0200 Subject: [PATCH 2/4] fix: assets/email_template.html --- assets/email_template.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/assets/email_template.html b/assets/email_template.html index 21a09edc..e8bda58a 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -3,11 +3,13 @@ + nf-core/rnavar Pipeline Report
+

nf-core/rnavar v${version}

From b9dc6e72ebaac1c3af54768158439ef22480d619 Mon Sep 17 00:00:00 2001 From: Praveen Date: Tue, 17 May 2022 15:04:13 +0200 Subject: [PATCH 3/4] Corrected nextflow version in manifest - nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 15257981..e3ab49f8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -235,7 +235,7 @@ manifest { homePage = 'https://github.com/nf-core/rnavar' description = 'GATK4 RNA variant calling pipeline' mainScript = 'main.nf' - nextflowVersion = '!>=21.10.3' + nextflowVersion = '>=21.10.3' version = '1.0dev' } From ba2893971d520fe95054eee06cd69a4b4c73162e Mon Sep 17 00:00:00 2001 From: Praveen Date: Tue, 17 May 2022 16:10:07 +0200 Subject: [PATCH 4/4] Update: nf-core tools --- README.md | 2 +- modules.json | 24 +++++++++---------- .../nf-core/modules/gatk4/applybqsr/main.nf | 6 ++--- .../modules/gatk4/baserecalibrator/main.nf | 6 ++--- .../modules/gatk4/bedtointervallist/main.nf | 6 ++--- .../gatk4/createsequencedictionary/main.nf | 6 ++--- .../modules/gatk4/haplotypecaller/main.nf | 6 ++--- .../modules/gatk4/indexfeaturefile/main.nf | 6 ++--- .../modules/gatk4/intervallisttools/main.nf | 6 ++--- .../modules/gatk4/markduplicates/main.nf | 8 +++---- .../nf-core/modules/gatk4/mergevcfs/main.nf | 6 ++--- .../modules/gatk4/splitncigarreads/main.nf | 6 ++--- .../modules/gatk4/variantfiltration/main.nf | 6 ++--- modules/nf-core/modules/snpeff/Dockerfile | 9 +++---- modules/nf-core/modules/snpeff/build.sh | 5 ++-- modules/nf-core/modules/snpeff/meta.yml | 12 ---------- 16 files changed, 55 insertions(+), 65 deletions(-) diff --git a/README.md b/README.md index 56c31fbc..a00e8e23 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ On release, automated continuous integration tests run the pipeline on a full-si | FastQC | 0.11.9 | | STAR | 2.7.9a | | Samtools | 1.15.1 | -| GATK | 4.2.5.0 | +| GATK | 4.2.6.1 | | SnpEff | 5.0 | | Ensembl VEP | 104.3 | | MultiQC | 1.12 | diff --git a/modules.json b/modules.json index 3f7997cc..c35f0779 100644 --- a/modules.json +++ b/modules.json @@ -16,37 +16,37 @@ "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" }, "gatk4/applybqsr": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/baserecalibrator": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/bedtointervallist": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/createsequencedictionary": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/haplotypecaller": { - "git_sha": "68f1c27169946f931ea4318911de5681f88b2961" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/indexfeaturefile": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/intervallisttools": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/markduplicates": { - "git_sha": "0511e7fbbfa4ba41940d33b687b1cc90227b4eb8" + "git_sha": "df2620cfc7e4c21b14ed03c1c928f09fbabf83c4" }, "gatk4/mergevcfs": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/splitncigarreads": { - "git_sha": "10ca39a86f1b227a5535238d02398fec686eba72" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gatk4/variantfiltration": { - "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449" + "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" }, "gffread": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" @@ -79,7 +79,7 @@ "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773" }, "snpeff": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_sha": "40dd662fd26c3eb3160b7c8cbbe9bff80bbe2c30" }, "star/align": { "git_sha": "1dddf1ce9443e3d93853d86e7a7aab52e5b4d614" diff --git a/modules/nf-core/modules/gatk4/applybqsr/main.nf b/modules/nf-core/modules/gatk4/applybqsr/main.nf index 7a64dab2..a0e2c45c 100644 --- a/modules/nf-core/modules/gatk4/applybqsr/main.nf +++ b/modules/nf-core/modules/gatk4/applybqsr/main.nf @@ -2,10 +2,10 @@ process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/modules/gatk4/baserecalibrator/main.nf b/modules/nf-core/modules/gatk4/baserecalibrator/main.nf index 766a8338..fb26d3da 100644 --- a/modules/nf-core/modules/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/modules/gatk4/baserecalibrator/main.nf @@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/modules/gatk4/bedtointervallist/main.nf b/modules/nf-core/modules/gatk4/bedtointervallist/main.nf index 118f535b..6224d9b3 100644 --- a/modules/nf-core/modules/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/modules/gatk4/bedtointervallist/main.nf @@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf b/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf index dbf37048..13fa9e81 100644 --- a/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf @@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: path fasta diff --git a/modules/nf-core/modules/gatk4/haplotypecaller/main.nf b/modules/nf-core/modules/gatk4/haplotypecaller/main.nf index 2cd9e7d4..6dd3f69e 100644 --- a/modules/nf-core/modules/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/modules/gatk4/haplotypecaller/main.nf @@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/modules/gatk4/indexfeaturefile/main.nf b/modules/nf-core/modules/gatk4/indexfeaturefile/main.nf index 90ff94e6..264f71ef 100644 --- a/modules/nf-core/modules/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/modules/gatk4/indexfeaturefile/main.nf @@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/modules/gatk4/intervallisttools/main.nf b/modules/nf-core/modules/gatk4/intervallisttools/main.nf index 1b9b37f4..7ab26c15 100644 --- a/modules/nf-core/modules/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/modules/gatk4/intervallisttools/main.nf @@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/modules/gatk4/markduplicates/main.nf b/modules/nf-core/modules/gatk4/markduplicates/main.nf index 2650925b..68e4a21a 100644 --- a/modules/nf-core/modules/gatk4/markduplicates/main.nf +++ b/modules/nf-core/modules/gatk4/markduplicates/main.nf @@ -1,11 +1,11 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" - label 'process_low' + label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/modules/gatk4/mergevcfs/main.nf b/modules/nf-core/modules/gatk4/mergevcfs/main.nf index 06ff3acb..964c1a3b 100644 --- a/modules/nf-core/modules/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/modules/gatk4/mergevcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/modules/gatk4/splitncigarreads/main.nf b/modules/nf-core/modules/gatk4/splitncigarreads/main.nf index 85e5daa8..456ec055 100644 --- a/modules/nf-core/modules/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/modules/gatk4/splitncigarreads/main.nf @@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/modules/gatk4/variantfiltration/main.nf b/modules/nf-core/modules/gatk4/variantfiltration/main.nf index 6beb87ef..cda06e11 100644 --- a/modules/nf-core/modules/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/modules/gatk4/variantfiltration/main.nf @@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/modules/snpeff/Dockerfile b/modules/nf-core/modules/snpeff/Dockerfile index 608716a4..d0e34757 100644 --- a/modules/nf-core/modules/snpeff/Dockerfile +++ b/modules/nf-core/modules/snpeff/Dockerfile @@ -8,15 +8,16 @@ LABEL \ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-snpeff-5.0/bin:$PATH - # Setup default ARG variables ARG GENOME=GRCh38 ARG SNPEFF_CACHE_VERSION=99 +ARG SNPEFF_TAG=99 + +# Add conda installation dir to PATH (instead of doing 'conda activate') +ENV PATH /opt/conda/envs/nf-core-snpeff-${SNPEFF_TAG}/bin:$PATH # Download Genome RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION} # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-snpeff-5.0 > nf-core-snpeff-5.0.yml +RUN conda env export --name nf-core-snpeff-${SNPEFF_TAG} > nf-core-snpeff-${SNPEFF_TAG}.yml diff --git a/modules/nf-core/modules/snpeff/build.sh b/modules/nf-core/modules/snpeff/build.sh index b94ffd69..2fccf9a8 100644 --- a/modules/nf-core/modules/snpeff/build.sh +++ b/modules/nf-core/modules/snpeff/build.sh @@ -9,10 +9,11 @@ build_push() { SNPEFF_TAG=$3 docker build \ + . \ -t nfcore/snpeff:${SNPEFF_TAG}.${GENOME} \ - software/snpeff/. \ --build-arg GENOME=${GENOME} \ - --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION} + --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION} \ + --build-arg SNPEFF_TAG=${SNPEFF_TAG} docker push nfcore/snpeff:${SNPEFF_TAG}.${GENOME} } diff --git a/modules/nf-core/modules/snpeff/meta.yml b/modules/nf-core/modules/snpeff/meta.yml index c191b9ac..2f0d866e 100644 --- a/modules/nf-core/modules/snpeff/meta.yml +++ b/modules/nf-core/modules/snpeff/meta.yml @@ -10,18 +10,6 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] -params: - - use_cache: - type: boolean - description: | - boolean to enable the usage of containers with cache - Enable the usage of containers with cache - Does not work with conda - - snpeff_tag: - type: value - description: | - Specify the tag for the container - https://hub.docker.com/r/nfcore/snpeff/tags input: - meta: type: map