From 0e97157f9ff40335d485990d8eff9be744bb4446 Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Mon, 11 Sep 2023 14:46:33 +0100 Subject: [PATCH 01/14] adding gene metrics module --- conf/modules/cnvkit.config | 9 ++++ modules.json | 6 +++ modules/nf-core/cnvkit/genemetrics/main.nf | 40 +++++++++++++++++ modules/nf-core/cnvkit/genemetrics/meta.yml | 43 +++++++++++++++++++ .../local/bam_variant_calling_cnvkit/main.nf | 2 + 5 files changed, 100 insertions(+) create mode 100644 modules/nf-core/cnvkit/genemetrics/main.nf create mode 100644 modules/nf-core/cnvkit/genemetrics/meta.yml diff --git a/conf/modules/cnvkit.config b/conf/modules/cnvkit.config index f77c6ef44..e17459369 100644 --- a/conf/modules/cnvkit.config +++ b/conf/modules/cnvkit.config @@ -47,4 +47,13 @@ process { pattern: "*{bed,cnn,cnr,cns,pdf,png}" ] } + // CNVKIT + withName: 'CNVKIT_GENEMETRICS' { + ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" }, + pattern: "*{tsv}" + ] + } } diff --git a/modules.json b/modules.json index 6732e1901..d9eb13ac2 100644 --- a/modules.json +++ b/modules.json @@ -75,6 +75,12 @@ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, + "cnvkit/genemetrics": { + "branch": "master", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"], + "patch": "modules/nf-core/cnvkit/genemetrics/cnvkit-genemetrics.diff" + }, "controlfreec/assesssignificance": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", diff --git a/modules/nf-core/cnvkit/genemetrics/main.nf b/modules/nf-core/cnvkit/genemetrics/main.nf new file mode 100644 index 000000000..d21c5b697 --- /dev/null +++ b/modules/nf-core/cnvkit/genemetrics/main.nf @@ -0,0 +1,40 @@ +process CNVKIT_GENEMETRICS { + tag "$meta.id" + label 'process_low' + + conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': + 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + + input: + tuple val(meta), path(cnr) + tuple val (meta), path(cns) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + //tuple val(meta), path("*.cnn"), emit: cnn + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: cnr.BaseName + def segments = cns ? "--segment ${cns[2]}" : "" + + """ + cnvkit.py \\ + genemetrics \\ + $cnr \\ + $segments \\ + --output ${prefix}.genemetrics.tsv \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml new file mode 100644 index 000000000..27e3c8c9e --- /dev/null +++ b/modules/nf-core/cnvkit/genemetrics/meta.yml @@ -0,0 +1,43 @@ +name: cnvkit_genemetrics +description: Copy number variant detection from high-throughput sequencing data +keywords: + - cnvkit + - genemetrics +tools: + - cnvkit: + description: | + CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. + homepage: https://cnvkit.readthedocs.io/en/stable/index.html + documentation: https://cnvkit.readthedocs.io/en/stable/index.html + licence: ["Apache-2.0"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cnr: + type: file + description: CNR file + pattern: "*.cnr" + - cns: + type: file + description: CNS file [Optional] + pattern: "*.cns" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - txt: + type: file + description: TXT file + pattern: "*.txt" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@marrip" \ No newline at end of file diff --git a/subworkflows/local/bam_variant_calling_cnvkit/main.nf b/subworkflows/local/bam_variant_calling_cnvkit/main.nf index d4b9e297b..742389e52 100644 --- a/subworkflows/local/bam_variant_calling_cnvkit/main.nf +++ b/subworkflows/local/bam_variant_calling_cnvkit/main.nf @@ -5,6 +5,7 @@ // A when clause condition is defined in the conf/modules.config to determine if the module should be run include { CNVKIT_BATCH } from '../../../modules/nf-core/cnvkit/batch/main' +include { CNVKIT_GENEMETRICS } from '../../../modules/nf-core/cnvkit/genemetrics/main' workflow BAM_VARIANT_CALLING_CNVKIT { take: @@ -18,6 +19,7 @@ workflow BAM_VARIANT_CALLING_CNVKIT { generate_pon = false CNVKIT_BATCH(cram, fasta, fasta_fai, targets, reference, generate_pon) + CNVKIT_GENEMETRICS(CNVKIT_BATCH.out.cnr, CNVKIT_BATCH.out.cns) versions = CNVKIT_BATCH.out.versions From cd43d532278611f45f36d2d52d87365038da28c4 Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Tue, 12 Sep 2023 09:24:29 +0100 Subject: [PATCH 02/14] updating documentation --- CHANGELOG.md | 9 +++++++++ docs/output.md | 5 ++++- modules.json | 10 +++++----- 3 files changed, 18 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c963ffbc..556a0b613 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,15 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [3.2.4](https://github.com/nf-core/sarek/releases/tag/3.2.4) - Gällivare + +Gällivare is a small lake next to Pierikjaure. + +### Added + +- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding genemetrics module + + ## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare Gällivare is a small lake next to Pierikjaure. diff --git a/docs/output.md b/docs/output.md index 1992c32a6..c0a446f6d 100644 --- a/docs/output.md +++ b/docs/output.md @@ -574,7 +574,8 @@ The file `.cnvs.txt` contains all segments predicte - file containing copy number segment information - `.call.cns` - file containing copy number segment information - +- `.genemetrics.tsv` + - file containing per gene copy number information (if input files are annotated)
@@ -602,6 +603,8 @@ The file `.cnvs.txt` contains all segments predicte - file containing copy number segment information - `.call.cns` - file containing copy number segment information +- `.genemetrics.tsv` + - file containing per gene copy number information (if input files are annotated)
#### Control-FREEC diff --git a/modules.json b/modules.json index d9eb13ac2..399c503f9 100644 --- a/modules.json +++ b/modules.json @@ -70,17 +70,17 @@ "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", "installed_by": ["modules"] }, - "cnvkit/reference": { - "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"] - }, "cnvkit/genemetrics": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"], "patch": "modules/nf-core/cnvkit/genemetrics/cnvkit-genemetrics.diff" }, + "cnvkit/reference": { + "branch": "master", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] + }, "controlfreec/assesssignificance": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", From e06866a3e82bc8138f49138cfc7b42bcde92ad0d Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Tue, 12 Sep 2023 09:52:44 +0100 Subject: [PATCH 03/14] updating changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 556a0b613..fe27df6c3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ Gällivare is a small lake next to Pierikjaure. ### Added -- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding genemetrics module +- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module ## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare From 5ec2ff30d62ad11174f21c24faa0f43000947f7a Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Tue, 12 Sep 2023 10:47:41 +0100 Subject: [PATCH 04/14] removing extra line from changelog --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b397350c4..5691b736e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -74,7 +74,6 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas | `grep` | 3.4 | 3.11 | | `multiqc` | 1.14 | 1.15 | | `tiddit` | 3.3.2 | 3.6.1 | ->>>>>>> 871acbc8a011c7af1172126a15fa6bd0bae0dd58 ## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare From ce1ed239f19f90b0b23cc13e0b247366e33f6301 Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Wed, 20 Sep 2023 10:57:55 +0100 Subject: [PATCH 05/14] moving changes to dev part of changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 72af6bc8a..1e5c6a501 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## dev - [#1246](https://github.com/nf-core/sarek/pull/1246) - Back to dev +- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module ### Added @@ -63,7 +64,6 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#1173](https://github.com/nf-core/sarek/pull/1173) - CI tests for VQSR track with stub runs - [#1122](https://github.com/nf-core/sarek/pull/1122), [#1196](https://github.com/nf-core/sarek/pull/1196) - Add `annotation cache` functionality - [#1184](https://github.com/nf-core/sarek/pull/1184) - Stub-based CI-test of Sentieon joint-germline variant-calling with VQSR -- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module ### Changed From 9b336420505069c4cbfd3c709386e475bd2be631 Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Wed, 20 Sep 2023 10:58:19 +0100 Subject: [PATCH 06/14] updating cnvkit and bioconda version --- modules/nf-core/cnvkit/genemetrics/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/cnvkit/genemetrics/main.nf b/modules/nf-core/cnvkit/genemetrics/main.nf index d21c5b697..99aad4a29 100644 --- a/modules/nf-core/cnvkit/genemetrics/main.nf +++ b/modules/nf-core/cnvkit/genemetrics/main.nf @@ -2,7 +2,7 @@ process CNVKIT_GENEMETRICS { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" From e9beaef44b276fa48d3089d6eccf1c0c09aa218a Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Wed, 20 Sep 2023 10:58:33 +0100 Subject: [PATCH 07/14] collecting versions --- subworkflows/local/bam_variant_calling_cnvkit/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/bam_variant_calling_cnvkit/main.nf b/subworkflows/local/bam_variant_calling_cnvkit/main.nf index 94674af96..a1c8ac80a 100644 --- a/subworkflows/local/bam_variant_calling_cnvkit/main.nf +++ b/subworkflows/local/bam_variant_calling_cnvkit/main.nf @@ -21,7 +21,8 @@ workflow BAM_VARIANT_CALLING_CNVKIT { CNVKIT_BATCH(cram, fasta, fasta_fai, targets, reference, generate_pon) CNVKIT_GENEMETRICS(CNVKIT_BATCH.out.cnr, CNVKIT_BATCH.out.cns) - versions = CNVKIT_BATCH.out.versions + versions = versions.mix(CNVKIT_BATCH.out.versions) + versions = versions.mix(CNVKIT_GENEMETRICS.out.versions) emit: versions // channel: [ versions.yml ] From 0ed20aa60c0f2315a0b7aa6e650f62557cf27c9c Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 16 Oct 2023 09:44:09 +0000 Subject: [PATCH 08/14] [automated] Fix linting with Prettier --- docs/output.md | 2 +- modules/nf-core/cnvkit/genemetrics/meta.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/output.md b/docs/output.md index b21539cc4..e82c3c173 100644 --- a/docs/output.md +++ b/docs/output.md @@ -719,7 +719,7 @@ The file `.cnvs.txt` contains all segments predicte - file containing copy number segment information - `.genemetrics.tsv` - file containing per gene copy number information (if input files are annotated) - +
Output files for tumor/normal samples diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml index 27e3c8c9e..1d8ee9e52 100644 --- a/modules/nf-core/cnvkit/genemetrics/meta.yml +++ b/modules/nf-core/cnvkit/genemetrics/meta.yml @@ -40,4 +40,4 @@ output: pattern: "versions.yml" authors: - - "@marrip" \ No newline at end of file + - "@marrip" From e8380eac80124e1e0c49a14e5f4aa0862bb576a9 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 16 Oct 2023 09:58:31 +0000 Subject: [PATCH 09/14] add version intilization --- CHANGELOG.md | 2 +- subworkflows/local/bam_variant_calling_cnvkit/main.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 61aedfdae..e529700c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,8 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## dev -- [#1246](https://github.com/nf-core/sarek/pull/1246) - Back to dev - [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module +- [#1246](https://github.com/nf-core/sarek/pull/1246) - Back to dev ### Added diff --git a/subworkflows/local/bam_variant_calling_cnvkit/main.nf b/subworkflows/local/bam_variant_calling_cnvkit/main.nf index a1c8ac80a..e4f6f3a15 100644 --- a/subworkflows/local/bam_variant_calling_cnvkit/main.nf +++ b/subworkflows/local/bam_variant_calling_cnvkit/main.nf @@ -16,6 +16,7 @@ workflow BAM_VARIANT_CALLING_CNVKIT { reference // channel: [] cnn main: + versions = Channel.empty() generate_pon = false CNVKIT_BATCH(cram, fasta, fasta_fai, targets, reference, generate_pon) From bf9c85859a72c38673914e1140860457582c12f9 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 16 Oct 2023 12:29:30 +0000 Subject: [PATCH 10/14] unpatch module, bump ressource request --- conf/base.config | 4 ++++ conf/modules/cnvkit.config | 1 + modules.json | 5 ++--- modules/nf-core/cnvkit/genemetrics/main.nf | 15 +++++++-------- modules/nf-core/cnvkit/genemetrics/meta.yml | 6 +++++- .../local/bam_variant_calling_cnvkit/main.nf | 4 +++- 6 files changed, 22 insertions(+), 13 deletions(-) mode change 100644 => 100755 modules/nf-core/cnvkit/genemetrics/main.nf mode change 100644 => 100755 modules/nf-core/cnvkit/genemetrics/meta.yml diff --git a/conf/base.config b/conf/base.config index db1175874..446e88b99 100644 --- a/conf/base.config +++ b/conf/base.config @@ -70,6 +70,10 @@ process { cpus = { check_max( 24 * task.attempt, 'cpus' ) } memory = { check_max( 30.GB * task.attempt, 'memory' ) } } + withName:'CNVKIT_BATCH' { + label = "process_high" + memory = { check_max( 36.GB * task.attempt, 'memory' ) } + } withName: 'GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK' { cpus = { check_max( 6 * task.attempt, 'cpus' ) } memory = { check_max( 30.GB * task.attempt, 'memory' ) } diff --git a/conf/modules/cnvkit.config b/conf/modules/cnvkit.config index e17459369..bf5ff6c6c 100644 --- a/conf/modules/cnvkit.config +++ b/conf/modules/cnvkit.config @@ -49,6 +49,7 @@ process { } // CNVKIT withName: 'CNVKIT_GENEMETRICS' { + ext.prefix = { "${cnr.baseName}.genemetrics" } ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } publishDir = [ mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index ba38ddebf..d5022b6f9 100644 --- a/modules.json +++ b/modules.json @@ -72,9 +72,8 @@ }, "cnvkit/genemetrics": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"], - "patch": "modules/nf-core/cnvkit/genemetrics/cnvkit-genemetrics.diff" + "git_sha": "3b63e1df297ef474b0070aa5fabb30d732173671", + "installed_by": ["modules"] }, "cnvkit/reference": { "branch": "master", diff --git a/modules/nf-core/cnvkit/genemetrics/main.nf b/modules/nf-core/cnvkit/genemetrics/main.nf old mode 100644 new mode 100755 index 99aad4a29..605899486 --- a/modules/nf-core/cnvkit/genemetrics/main.nf +++ b/modules/nf-core/cnvkit/genemetrics/main.nf @@ -4,12 +4,11 @@ process CNVKIT_GENEMETRICS { conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: - tuple val(meta), path(cnr) - tuple val (meta), path(cns) + tuple val(meta), path(cnr), path(cns) output: tuple val(meta), path("*.tsv"), emit: tsv @@ -21,15 +20,15 @@ process CNVKIT_GENEMETRICS { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: cnr.BaseName - def segments = cns ? "--segment ${cns[2]}" : "" + def prefix = task.ext.prefix ?: "${meta.id}" + def segments = cns ? "--segment ${cns}" : "" """ cnvkit.py \\ genemetrics \\ $cnr \\ $segments \\ - --output ${prefix}.genemetrics.tsv \\ + --output ${prefix}.tsv \\ $args cat <<-END_VERSIONS > versions.yml @@ -37,4 +36,4 @@ process CNVKIT_GENEMETRICS { cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml old mode 100644 new mode 100755 index 1d8ee9e52..115a4a87b --- a/modules/nf-core/cnvkit/genemetrics/meta.yml +++ b/modules/nf-core/cnvkit/genemetrics/meta.yml @@ -2,7 +2,9 @@ name: cnvkit_genemetrics description: Copy number variant detection from high-throughput sequencing data keywords: - cnvkit - - genemetrics + - bam + - fasta + - copy number tools: - cnvkit: description: | @@ -40,4 +42,6 @@ output: pattern: "versions.yml" authors: + - "@adamrtalbot" - "@marrip" + - "@priesgo" diff --git a/subworkflows/local/bam_variant_calling_cnvkit/main.nf b/subworkflows/local/bam_variant_calling_cnvkit/main.nf index e4f6f3a15..c6b93d33c 100644 --- a/subworkflows/local/bam_variant_calling_cnvkit/main.nf +++ b/subworkflows/local/bam_variant_calling_cnvkit/main.nf @@ -20,7 +20,9 @@ workflow BAM_VARIANT_CALLING_CNVKIT { generate_pon = false CNVKIT_BATCH(cram, fasta, fasta_fai, targets, reference, generate_pon) - CNVKIT_GENEMETRICS(CNVKIT_BATCH.out.cnr, CNVKIT_BATCH.out.cns) + + ch_genemetrics = CNVKIT_BATCH.out.cnr.join(CNVKIT_BATCH.out.cns).map{ meta, cnr, cns -> [meta, cnr, cns[2]]} + CNVKIT_GENEMETRICS(ch_genemetrics) versions = versions.mix(CNVKIT_BATCH.out.versions) versions = versions.mix(CNVKIT_GENEMETRICS.out.versions) From 527ddb12744b6dce4f222c0304a730f0563ea55d Mon Sep 17 00:00:00 2001 From: grantn5 <127763095+grantn5@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:07:56 +0100 Subject: [PATCH 11/14] Update docs/output.md Co-authored-by: Maxime U Garcia --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index e82c3c173..b21539cc4 100644 --- a/docs/output.md +++ b/docs/output.md @@ -719,7 +719,7 @@ The file `.cnvs.txt` contains all segments predicte - file containing copy number segment information - `.genemetrics.tsv` - file containing per gene copy number information (if input files are annotated) -
+
Output files for tumor/normal samples From fef4d51803772c84ffcf1c71bfca04b41ffaa321 Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Mon, 16 Oct 2023 15:10:30 +0000 Subject: [PATCH 12/14] updating changelog --- CHANGELOG.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e529700c8..2244906bb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,11 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## dev -- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module -- [#1246](https://github.com/nf-core/sarek/pull/1246) - Back to dev - ### Added +- [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module - [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline. - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev From fb7cd94615ad2d7282f715a52366381c8c58a8d1 Mon Sep 17 00:00:00 2001 From: Grant Neilson Date: Mon, 16 Oct 2023 15:28:42 +0000 Subject: [PATCH 13/14] prettier run --- CHANGELOG.md | 1 - docs/output.md | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b56ff669..adf39f64d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - - [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module - [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline. - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev diff --git a/docs/output.md b/docs/output.md index b21539cc4..e82c3c173 100644 --- a/docs/output.md +++ b/docs/output.md @@ -719,7 +719,7 @@ The file `.cnvs.txt` contains all segments predicte - file containing copy number segment information - `.genemetrics.tsv` - file containing per gene copy number information (if input files are annotated) -
+
Output files for tumor/normal samples From 9ea1aad711617869d9472fa02a4172dfd9f3446c Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 16 Oct 2023 16:22:20 +0000 Subject: [PATCH 14/14] fix spelling --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index adf39f64d..0944a04b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module -- [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline. +- [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev ### Changed