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Merge pull request #155 from CenterForMedicalGeneticsGhent/dev
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Release PR v1.4.0
nvnieuwk authored Dec 6, 2023
2 parents 1e8a16e + 649c2b9 commit 384ed60
Showing 261 changed files with 12,554 additions and 4,136 deletions.
1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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@@ -2,6 +2,7 @@
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
3 changes: 2 additions & 1 deletion .github/workflows/ci.yml
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@@ -27,7 +27,8 @@ jobs:
- "23.04.0"
- "latest-everything"
test:
- "default"
- "vardict"
- "haplotypecaller"
- "fails"
- "annotate_test"
- "filter_test"
3 changes: 1 addition & 2 deletions .github/workflows/linting.yml
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@@ -70,8 +70,7 @@ jobs:

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install nf-core
python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
- name: Run nf-core lint
env:
68 changes: 68 additions & 0 deletions .github/workflows/release-announcments.yml
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name: release-announcements
# Automatic release toot and tweet anouncements
on:
release:
types: [published]
workflow_dispatch:

jobs:
toot:
runs-on: ubuntu-latest
steps:
- uses: rzr/fediverse-action@master
with:
access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
host: "mstdn.science" # custom host if not "mastodon.social" (default)
# GitHub event payload
# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
message: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
send-tweet:
runs-on: ubuntu-latest

steps:
- uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: pip install tweepy==4.14.0
- name: Send tweet
shell: python
run: |
import os
import tweepy
client = tweepy.Client(
access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
)
tweet = os.getenv("TWEET")
client.create_tweet(text=tweet)
env:
TWEET: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}

bsky-post:
runs-on: ubuntu-latest
steps:
- uses: zentered/bluesky-post-action@v0.0.2
with:
post: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
env:
BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
#
9 changes: 7 additions & 2 deletions .nf-core.yml
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@@ -1,4 +1,3 @@
repository_type: pipeline
lint:
files_exist:
- CODE_OF_CONDUCT.md
@@ -32,5 +31,11 @@ lint:
- lib/NfcoreTemplate.groovy
- .prettierignore
- LICENSE
actions_ci: false
pipeline_name_conventions: false
actions_ci: false
repository_type: pipeline
template:
author: nvnieuwk
description: A nextflow pipeline for calling and annotating variants
name: nf-cmgg-germline
prefix: CenterForMedicalGeneticsGhent
2 changes: 1 addition & 1 deletion .prettierignore
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@@ -2,7 +2,7 @@ email_template.html
adaptivecard.json
slackreport.json
.nextflow*
.nf-test/
.nf-test*
work/
data/
results/
25 changes: 25 additions & 0 deletions CHANGELOG.md
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@@ -3,6 +3,31 @@
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).

## v1.4.0 - Kingly Kortrijk - [December 6 2023]

### New Features

1. Added the `--callers` parameter to specify the variant caller to use. Currently only `haplotypecaller` and `vardict` are supported.
2. Added the `vardict` variant caller.
3. Added the `--vardict_min_af` parameter to specify the minimum allele frequency for `vardict`. This option is also available in the samplesheet as `vardict_min_af` to set it dynamically per sample.
4. Added the `--output_genomicsdb` option to specify whether a GenomicsDB should be outputted or not. This will be `true` when using `only_merge`.
5. Added `--normalize` options for decomposing and normalizing of variants after calling and genotyping.
6. Added `WGS`, `WES`, `SeqCap`, `HyperCap` and `seqplorer` profiles that can be used to set the default parameters for these types of runs.

### Improvements

1. Refactored the pipeline to accomodate future additions of variant callers and genotypers
2. Removed a lot of unnecessary bloat
3. Improved GenomicsDBImport (can now be multithreaded and runs a lot faster). This will make very big runs more possible.
4. Changed `coverage_fast` to `mosdepth_slow`, reversing the effect of the parameter. By default mosdepth will now be run with `--fast-mode`. This can be disabled using the new `mosdepth_slow` parameter.
5. Automatically merge the regions that are within 150 bps of eachother for the variant calling. This way it's ensured that indel calling happens correctly.

### Fixes

1. Fixed an issue with the outputting of the validation PNG files, now all three types of PNGs are outputted.
2. Fixed a small issue where VCFs without a sample created by the callers could not be used by `bcftools concat`, these files will now be filtered from the input of the command.
3. Removed the `--maxentscan` parameter because this file is automatically present in the container

## v1.3.0 - Happy Hasselt - [July 10 2023]

### New Features
33 changes: 19 additions & 14 deletions README.md
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@@ -7,48 +7,53 @@

## Introduction

**nf-cmgg-germline** is a bioinformatics best-practice analysis pipeline for calling, joint-genotyping and annotating small variants variants for WGS and WES data. It uses HaplotypeCaller to call variants, GenotypeGVCFs to genotype and EnsemblVEP to annotate.
**nf-cmgg-germline** is a bioinformatics best-practice analysis pipeline for calling, joint-genotyping and annotating small variants variants for WGS and WES data. It uses HaplotypeCaller and/or Vardict to call variants, GenotypeGVCFs to genotype and EnsemblVEP to annotate.

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

## Pipeline summary

![metro graph](docs/images/nf-cmgg-germline_metro.png)

:::note
If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
with `-profile test` before running the workflow on actual data.
:::

## Quick Start

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.5`)
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=23.04.0`)
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.

`samplesheet.csv`:

```csv
sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
sample,family,cram,crai
SAMPLE_1,FAMILY_1,SAMPLE_1.cram,SAMPLE_1.crai
```

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Each row represents a single sample to be analysed. More information can be found in the [usage](docs/usage.md) documentation.

-->

Now, you can run the pipeline using:

<!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->

```bash
nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-germline --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-germline --input samplesheet.csv --outdir <OUTDIR> --genome GRCh38 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```

> **Warning:**
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
:::warning
Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
:::

## Credits

nf-cmgg-germline was originally written and is maintained by @nvnieuwk.
nf-cmgg-germline was originally written and is maintained by [@nvnieuwk](https://github.com/nvnieuwk).

Special thanks to @matthdsm for the many tips and feedback and to @mvheetve for testing the pipeline.
Special thanks to [@matthdsm](https://github.com/matthdsm) for the many tips and feedback and to [@mvheetve](https://github.com/mvheetve) for testing the pipeline.

## Contributions and Support

2 changes: 1 addition & 1 deletion assets/multiqc_config.yml
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@@ -1,5 +1,5 @@
report_comment: >
This report has been generated by the <a href="https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline/1.3.0" target="_blank">CenterForMedicalGeneticsGhent/nf-cmgg-germline</a>
This report has been generated by the <a href="https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline/1.4.0" target="_blank">CenterForMedicalGeneticsGhent/nf-cmgg-germline</a>
analysis pipeline.
report_section_order:
"CenterForMedicalGeneticsGhent-nf-cmgg-germline-methods-description":
6 changes: 3 additions & 3 deletions assets/samplesheet.csv
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@@ -1,3 +1,3 @@
sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed
DNA049572,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline/dev/assets/test.ped,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz.tbi,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed
NA24385D2_NVQ_034,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test2.vcf.gz,,
sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed,vardict_min_af
DNA049572,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline/dev/assets/test.ped,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz.tbi,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01
NA24385D2_NVQ_034,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test2.vcf.gz,,,
31 changes: 22 additions & 9 deletions assets/schema_input.json
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"cram": {
"type": "string",
"pattern": "^\\S+\\.cram$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"crai": {
"type": "string",
"pattern": "^\\S+\\.crai$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"gvcf": {
"type": "string",
"pattern": "^\\S+vcf(.gz)?$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"tbi": {
"type": "string",
"pattern": "^\\S+\\.tbi$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"roi": {
"type": "string",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"ped": {
"type": "string",
"pattern": "^\\S+\\.ped$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"truth_vcf": {
"type": "string",
"pattern": "^\\S+\\.vcf\\.gz$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"truth_tbi": {
"type": "string",
"pattern": "^\\S+\\.tbi$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"truth_bed": {
"type": "string",
"pattern": "^\\S+\\.bed$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"vardict_min_af": {
"type": "number",
"meta": ["vardict_min_af"]
}
},
"required": ["sample"]
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20 changes: 20 additions & 0 deletions conf/HyperCap.config
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/*
========================================================================================
Nextflow config file for HyperCap runs
========================================================================================
*/

params {
callers = "vardict"
filter = true
normalize = true
annotate = true
vcfanno = true
scatter_count = 5
vep_dbnsfp = true
vep_spliceai = true
vep_spliceregion = true
vep_mastermind = true
vep_maxentscan = true
vep_eog = true
}
12 changes: 12 additions & 0 deletions conf/SeqCap.config
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/*
========================================================================================
Nextflow config file for SeqCap runs
========================================================================================
*/

params {
callers = "vardict"
filter = true
normalize = true
scatter_count = 14
}
11 changes: 11 additions & 0 deletions conf/WES.config
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/*
========================================================================================
Nextflow config file for WES runs
========================================================================================
*/

params {
roi = "${params.genomes_base}/Hsapiens/GRCh38.p14/regions/CMGG_WES_analysis_ROI_v4.bed"
scatter_count = 14

}
9 changes: 9 additions & 0 deletions conf/WGS.config
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/*
========================================================================================
Nextflow config file for WGS runs
========================================================================================
*/

params {
scatter_count = 30
}
483 changes: 325 additions & 158 deletions conf/modules.config

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4 changes: 2 additions & 2 deletions conf/nf_test.config
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@@ -12,8 +12,7 @@ params {
max_time = '6.h'

// Input data
input = "${params.baseDir}/tests/inputs/samplesheet.csv"
outdir = "${params.outputDir}"
input = "${baseDir}/tests/inputs/samplesheet.csv"

// Genome references
genomes_ignore = true
@@ -23,6 +22,7 @@ params {
// Required params
scatter_count = 2
project = "test"
callers = "haplotypecaller,vardict"

// Extras
vep_merged = false
23 changes: 23 additions & 0 deletions conf/seqplorer.config
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@@ -0,0 +1,23 @@
/*
========================================================================================
Nextflow config file for runs that need to be imported in seqplorer
========================================================================================
*/

params {
filter = true
decompose = true
normalize = true

annotate = true
vep_dbnsfp = true
vep_spliceai = true
vep_mastermind = true
vep_eog = true
vep_maxentscan = true
vep_spliceregion = true


gemini = true

}
1 change: 1 addition & 0 deletions conf/test.config
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@@ -43,6 +43,7 @@ params {
add_ped = true
vep_chunk_size = 10000
project = "test"
normalize = true

vep_merged = false

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43 changes: 30 additions & 13 deletions docs/output.md
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@@ -4,31 +4,48 @@

This document describes the output produced by the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level output directory (specified by `--outdir <DIR>`). This is an example output when the pipeline has been run for a WGS sample called `SAMPLE_1` and a WES sample called `SAMPLE_2` which form a family called `FAMILY_1`. The output consists of 4 directories: `ready`, `individuals`, `multiqc_reports` and `pipeline_info`.
The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level output directory (specified by `--outdir <DIR>`). This is an example output when the pipeline has been run for a WGS sample called `SAMPLE_1` and a WES sample called `SAMPLE_2` which form a family called `FAMILY_1`. The output consists of 4 directories: `yyyy-MM-dd_project_name`, `individuals`, `multiqc_reports` and `pipeline_info`.

- The folder `yyyy-MM-dd_project_name` contains the joint-genotyped VCFs of every family along with the output from `bcftools stats` and the somalier plots generated from these files. It also contains a PED file (automatically generated if it wasn't supplied in the samplesheet) and the extended version of the PED file as a `.samples.tsv` file. It also contains the BED regions used in the scatter/gather process for joint-genotyping. The `yyyy-MM-dd` part of the folder will be the date of the analysis and `project_name` can be specified by `--project <STRING>`. If this parameter isn't specified, the mnemonic name of the nextflow run will be used instead.
- The folder `yyyy-MM-dd_project_name` contains the final outputs (either joint-genotyped VCFs or single-sample VCFs dependent on what callers have been used). Alongside the VCFs, a generated PED file, BED file for joint-genotyped samples and gemini database (`--gemini`) are also present. The `yyyy-MM-dd` part of the folder will be the date of the analysis and `project_name` can be specified by `--project <STRING>`. If this parameter isn't specified, the mnemonic name of the nextflow run will be used instead.
- The sample folders contain the GVCF and index of every individual along with the output of `bcftools stats` generated from these files and the mosdepth output. It also contains the BED regions used in the scatter/gather process for variant calling. If a validation has been performed all results will also be in the subfolder `validation`.
- The folder `multiqc_reports` contains all the MultiQC report files
- The folder `pipeline_info` contains reports on the execution of the pipeline

```bash
results/
├── yyyy-MM-dd_project_name/
│ └── FAMILY_1/
│ ├── FAMILY_1.vcf.gz
│ ├── FAMILY_1.vcf.gz.tbi
│ ├── FAMILY_1.ped
│ ├── FAMILY_1.samples.tsv
│ ├── FAMILY_1.bed
│ ├── FAMILY_1/
│ │ ├── FAMILY_1.caller.vcf.gz
│ │ ├── FAMILY_1.caller.vcf.gz.tbi
│ │ ├── FAMILY_1.caller.ped
│ │ ├── FAMILY_1.caller.db
│ │ ├── FAMILY_1.bed
│ │ └── reports/
│ │ ├── FAMILY_1.caller.bcftools_stats.txt
│ │ └── FAMILY_1.caller.somalier.html
│ ├── SAMPLE_1/
│ │ ├── SAMPLE_1.caller.vcf.gz
│ │ ├── SAMPLE_1.caller.vcf.gz.tbi
│ │ ├── SAMPLE_1.caller.ped
│ │ ├── SAMPLE_1.caller.db
│ │ └── reports/
│ │ ├── SAMPLE_1.caller.bcftools_stats.txt
│ │ └── SAMPLE_1.caller.somalier.html
│ └── SAMPLE_2/
│ ├── SAMPLE_2.caller.vcf.gz
│ ├── SAMPLE_2.caller.vcf.gz.tbi
│ ├── SAMPLE_2.caller.ped
│ ├── SAMPLE_2.caller.db
│ └── reports/
│ └── FAMILY_1.bcftools_stats.txt
│ ├── SAMPLE_2.caller.bcftools_stats.txt
│ └── SAMPLE_2.caller.somalier.html
├── SAMPLE_1/
│ ├── SAMPLE_1.quantized.bed.gz
│ ├── SAMPLE_1.quantized.bed.gz.csi
│ ├── SAMPLE_1.mosdepth.global.dist.txt
│ ├── SAMPLE_1.summary.txt
│ ├── SAMPLE_1.g.vcf.gz
│ ├── SAMPLE_1.g.vcf.gz.tbi
│ ├── SAMPLE_1.caller.g.vcf.gz
│ ├── SAMPLE_1.caller.g.vcf.gz.tbi
│ ├── validation/
│ └── reports/
│ └── SAMPLE_1.bcftools_stats.txt
@@ -41,8 +58,8 @@ results/
│ ├── SAMPLE_2.mosdepth.region.dist.txt
│ ├── SAMPLE_2.summary.txt
│ ├── SAMPLE_2.bed
│ ├── SAMPLE_2.g.vcf.gz
│ ├── SAMPLE_2.g.vcf.gz.tbi
│ ├── SAMPLE_2.caller.g.vcf.gz
│ ├── SAMPLE_2.caller.g.vcf.gz.tbi
│ ├── validation/
│ └── reports/
│ └── SAMPLE_2.bcftools_stats.txt
54 changes: 28 additions & 26 deletions docs/parameters.md

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61 changes: 35 additions & 26 deletions docs/usage.md
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
## Samplesheet input

You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It can be either a CSV, TSV or YAML file.
You will need to create a samplesheet with information with the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It can be either a CSV, TSV or YAML file.

```bash
--input '[path to samplesheet file]'
@@ -19,18 +19,18 @@ The `sample` identifiers have to be the same when you have re-sequenced the same
#### CSV

```csv
sample,family,cram,crai,ped,truth_vcf,truth_tbi,roi
SAMPLE_1,FAMILY_1,SAMPLE_1.cram,SAMPLE_1.crai,FAMILY_1.ped,SAMPLE_1.truth.vcf.gz,SAMPLE_1.truth.vcf.gz.tbi,SAMPLE_1.bed
SAMPLE_2,FAMILY_1,SAMPLE_2.cram,SAMPLE_2.crai,,SAMPLE_2.truth.vcf.gz,,SAMPLE_2.bed
SAMPLE_3,,SAMPLE_3.cram,,,,,
sample,family,cram,crai,ped,truth_vcf,truth_tbi,roi,vardict_min_af
SAMPLE_1,FAMILY_1,SAMPLE_1.cram,SAMPLE_1.crai,FAMILY_1.ped,SAMPLE_1.truth.vcf.gz,SAMPLE_1.truth.vcf.gz.tbi,SAMPLE_1.bed,0.1
SAMPLE_2,FAMILY_1,SAMPLE_2.cram,SAMPLE_2.crai,,SAMPLE_2.truth.vcf.gz,,SAMPLE_2.bed,0.01
SAMPLE_3,,SAMPLE_3.cram,,,,,,
```

#### TSV

```tsv
sample family cram crai ped truth_vcf truth_tbi roi
SAMPLE_1 FAMILY_1 SAMPLE_1.cram SAMPLE_1.crai FAMILY_1.ped SAMPLE_1.truth.vcf.gz SAMPLE_1.truth.vcf.gz.tbi SAMPLE_1.bed
SAMPLE_2 FAMILY_1 SAMPLE_2.cram SAMPLE_2.crai SAMPLE_2.truth.vcf.gz SAMPLE_2.bed
sample family cram crai ped truth_vcf truth_tbi roi vardict_min_af
SAMPLE_1 FAMILY_1 SAMPLE_1.cram SAMPLE_1.crai FAMILY_1.ped SAMPLE_1.truth.vcf.gz SAMPLE_1.truth.vcf.gz.tbi SAMPLE_1.bed 0.1
SAMPLE_2 FAMILY_1 SAMPLE_2.cram SAMPLE_2.crai SAMPLE_2.truth.vcf.gz SAMPLE_2.bed 0.01
SAMPLE_3 SAMPLE_3.cram
```

@@ -45,13 +45,15 @@ SAMPLE_3 SAMPLE_3.cram
truth_vcf: SAMPLE_1.truth.vcf.gz
truth_tbi: SAMPLE_1.truth.vcf.gz.tbi
roi: SAMPLE_1.bed
vardict_min_af: 0.1
- sample: SAMPLE_2
family: FAMILY_1
cram: SAMPLE_2.cram
crai: SAMPLE_2.crai
ped: FAMILY_1.ped
truth_vcf: SAMPLE_2.truth.vcf.gz
roi: SAMPLE_2.bed
vardict_min_af: 0.01
- sample: SAMPLE_3
cram: SAMPLE_3.cram
```
@@ -60,16 +62,17 @@ SAMPLE_3 SAMPLE_3.cram
The samplesheet can have following columns:
| Column | Description |
| ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `sample` | MANDATORY - Custom sample name. This entry has to be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
| `family` | OPTIONAL - The family ID of the specified sample. This field is optional, as the family id can also be extracted from the `ped` file. If no `ped` file and `family` ID are supplied, the `family` ID defaults to the `sample` ID (which means that the resulting VCF will be single-sample). Spaces in family names are automatically converted to underscores (`_`). |
| `cram` | MANDATORY - Full path to CRAM file to call variants from. File has to have the extension `.cram` |
| `crai` | OPTIONAL - Full path to CRAM index file. File has to have the extension `.crai`. |
| `ped` | OPTIONAL - Full path to PED file containing the relational information between samples in the same family. File has to have the extension `.ped`. |
| `truth_vcf` | OPTIONAL - Full path to the VCF containing all the truth variants of the current sample. The validation subworkflow will be run when this file is supplied and the `--validate true` flag has been given. File has to have the extension `.vcf.gz` |
| `truth_tbi` | OPTIONAL - Full path to the index of the truth VCF. This file can either be supplied by the user or generated by the pipeline. File has to have the extensions `.tbi` |
| `roi` | OPTIONAL - Full path to a BED file containing the regions of interest for the current sample to call on. When this file is given, the pipeline will run this sample in WES mode. (The flag `--roi <path>` can also be given to run WES mode for all samples using the file specified by the flag) File has to have the extension `.bed` or `.bed.gz`. |
| Column | Description |
| ---------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `sample` | MANDATORY - Custom sample name. This entry has to be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
| `family` | OPTIONAL - The family ID of the specified sample. This field is optional, as the family id can also be extracted from the `ped` file. If no `ped` file and `family` ID are supplied, the `family` ID defaults to the `sample` ID (which means that the resulting VCF will be single-sample). Spaces in family names are automatically converted to underscores (`_`). |
| `cram` | MANDATORY - Full path to CRAM file to call variants from. File has to have the extension `.cram` |
| `crai` | OPTIONAL - Full path to CRAM index file. File has to have the extension `.crai`. |
| `ped` | OPTIONAL - Full path to PED file containing the relational information between samples in the same family. File has to have the extension `.ped`. |
| `truth_vcf` | OPTIONAL - Full path to the VCF containing all the truth variants of the current sample. The validation subworkflow will be run when this file is supplied and the `--validate true` flag has been given. File has to have the extension `.vcf.gz` |
| `truth_tbi` | OPTIONAL - Full path to the index of the truth VCF. This file can either be supplied by the user or generated by the pipeline. File has to have the extensions `.tbi` |
| `roi` | OPTIONAL - Full path to a BED file containing the regions of interest for the current sample to call on. When this file is given, the pipeline will run this sample in WES mode. (The flag `--roi <path>` can also be given to run WES mode for all samples using the file specified by the flag) File has to have the extension `.bed` or `.bed.gz`. |
| `vardict_min_af` | OPTIONAL - The minimum AF value to use for the vardict variant caller (`--callers vardict`). This can be set in the samplesheet when it differs for all samples. A default can be set using the `--vardict_min_af` parameter (whichs defaults to 0.1) |

An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.

@@ -78,7 +81,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
The typical command for running the pipeline is as follows:

```bash
nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-germline --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-germline --input ./samplesheet.csv --outdir ./results --genome GRCh38 -profile docker
```

This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -96,7 +99,9 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than

Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.

> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
:::warning
Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
:::

The above pipeline run specified with a params file in yaml format:

@@ -109,12 +114,10 @@ with `params.yaml` containing:
```yaml
input: './samplesheet.csv'
outdir: './results/'
genome: 'GRCh37'
genome: 'GRCh38'
<...>
```

You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).

### Updating the pipeline

When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline. You can also add the `-latest` argument to your run command to automatically fetch the latest version on every run:
@@ -133,19 +136,25 @@ This version number will be logged in reports when you run the pipeline, so that

To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.

> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
:::tip
If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
:::

## Core Nextflow arguments

> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
:::note
These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
:::

### `-profile`

Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.

Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.

> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
:::info
We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
:::

The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).

3 changes: 0 additions & 3 deletions hpc_input/NA12878.ped

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3 changes: 0 additions & 3 deletions hpc_input/samplesheet_full.csv

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3 changes: 0 additions & 3 deletions hpc_input/samplesheet_small.csv

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60 changes: 60 additions & 0 deletions lib/DynamicContainers.groovy
Original file line number Diff line number Diff line change
@@ -0,0 +1,60 @@
class DynamicContainers {
static String apiUrl = "https://api.biocontainers.pro/ga4gh/trs/v2"

public static String findLatest(String containerName, Double version, String type="docker") {
this.findLatest(containerName, version as String, type)
}

public static String findLatest(String containerName, Float version, String type="docker") {
this.findLatest(containerName, version as String, type)
}

public static String findLatest(String containerName, Integer version, String type="docker") {
this.findLatest(containerName, version as String, type)
}

public static String findLatest(String containerName, String version, String type="docker") {
type = type ? type.toLowerCase() : "docker"
def String url = "${this.apiUrl}/tools/${containerName}/versions/${containerName}-${version}"
def biocontainersGet = new URL(url).openConnection()
biocontainersGet.setRequestProperty("accept", "application/json")
def getRC = biocontainersGet.getResponseCode()

if (getRC != 200) { return null }

def parser = new groovy.json.JsonSlurper()
def jsonResponse = parser.parseText(biocontainersGet.getInputStream().getText())

def ArrayList images = jsonResponse["images"].findAll { it["image_type"].toLowerCase() == type }
if(images.size() > 1 && type != "conda") {
return this.getLatestImage(images)
}
else if(images.size() == 0 && type == "singularity") {
images = jsonResponse["images"].findAll { it["image_type"].toLowerCase() == "docker" }
return this.getLatestImage(images)
}
else {
return images[0]["image_name"]
}

}

static String getLatestImage(ArrayList images) {
def Date latestTime
def String latestImage
for(image : images) {
def Integer year = image["updated"].split("-")[0] as Integer
def Integer month = image["updated"].split("-")[1] as Integer
def Integer day = image["updated"].split("-")[2].split("T")[0] as Integer
def Integer hour = image["updated"].split("T")[1].split(":")[0] as Integer
def Integer minutes = image["updated"].split("T")[1].split(":")[1] as Integer
def Integer seconds = image["updated"].split("T")[1].split(":")[2].split("Z")[0] as Integer
def Date time = new Date(year, month, day, hour, minutes, seconds)
if (time > latestTime) {
latestTime = time
latestImage = image["image_name"]
}
}
return latestImage
}
}
9 changes: 9 additions & 0 deletions lib/GlobalVariables.groovy
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
// A class that contains some variables that need to be globally accesible

class GlobalVariables {
// The available callers
public static List availableCallers = ["haplotypecaller", "vardict"]

public static List gvcfCallers = ["haplotypecaller"]

}
17 changes: 16 additions & 1 deletion lib/NfcoreTemplate.groovy
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
//

import org.yaml.snakeyaml.Yaml
import static groovy.json.JsonOutput.toJson
import groovy.json.JsonOutput

class NfcoreTemplate {

@@ -223,6 +223,21 @@ class NfcoreTemplate {
}
}

//
// Dump pipeline parameters in a json file
//
public static void dump_parameters(workflow, params) {
def output_d = new File("${params.outdir}/pipeline_info/")
if (!output_d.exists()) {
output_d.mkdirs()
}

def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
def output_pf = new File(output_d, "params_${timestamp}.json")
def jsonStr = JsonOutput.toJson(params)
output_pf.text = JsonOutput.prettyPrint(jsonStr)
}

//
// Print pipeline summary on completion
//
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18 changes: 9 additions & 9 deletions modules/local/filter_beds/main.nf
Original file line number Diff line number Diff line change
@@ -2,17 +2,17 @@ process FILTER_BEDS {
tag "$meta.id"
label 'process_single'

conda "bioconda::tabix=1.11"
conda "bioconda::bedtools=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' :
'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }"

input:
tuple val(meta), path(bed)

output:
tuple val(meta), path('*.bed.gz'), emit: bed
path "versions.yml" , emit: versions
tuple val(meta), path('*.bed'), emit: bed
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
@@ -24,23 +24,23 @@ process FILTER_BEDS {

def unzip = bed.extension == "gz" ? "zcat" : "cat"
"""
${unzip} ${bed} | grep -v NO_COVERAGE | bgzip --threads ${task.cpus} --stdout > ${prefix}.bed.gz
${unzip} ${bed} | grep -v NO_COVERAGE | bedtools merge ${args} > ${prefix}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.bed.gz
touch ${prefix}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
}
6 changes: 3 additions & 3 deletions modules/local/merge_beds.nf
Original file line number Diff line number Diff line change
@@ -2,10 +2,10 @@ process MERGE_BEDS {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bedtools=2.30.0"
conda "bioconda::bedtools=2.31.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' :
'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }"

input:
tuple val(meta), path(bed, stageAs: "?/*")
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6 changes: 3 additions & 3 deletions modules/nf-core/bedtools/split/main.nf

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9 changes: 4 additions & 5 deletions modules/nf-core/bedtools/split/meta.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/environment.yml

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6 changes: 3 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf

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7 changes: 4 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/meta.yml

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38 changes: 38 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test

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2 changes: 2 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml

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19 changes: 19 additions & 0 deletions modules/nf-core/ensemblvep/download/ensemblvep-download.diff

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7 changes: 7 additions & 0 deletions modules/nf-core/ensemblvep/download/environment.yml

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44 changes: 44 additions & 0 deletions modules/nf-core/ensemblvep/download/main.nf

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45 changes: 45 additions & 0 deletions modules/nf-core/ensemblvep/download/meta.yml

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23 changes: 14 additions & 9 deletions modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff

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6 changes: 2 additions & 4 deletions modules/nf-core/ensemblvep/vep/main.nf

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7 changes: 7 additions & 0 deletions modules/nf-core/gatk4/calibratedragstrmodel/environment.yml

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5 changes: 3 additions & 2 deletions modules/nf-core/gatk4/calibratedragstrmodel/main.nf

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10 changes: 3 additions & 7 deletions modules/nf-core/gatk4/calibratedragstrmodel/meta.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/gatk4/composestrtablefile/environment.yml

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5 changes: 3 additions & 2 deletions modules/nf-core/gatk4/composestrtablefile/main.nf

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7 changes: 3 additions & 4 deletions modules/nf-core/gatk4/composestrtablefile/meta.yml

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5 changes: 3 additions & 2 deletions modules/nf-core/gatk4/createsequencedictionary/main.nf

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7 changes: 5 additions & 2 deletions modules/nf-core/gatk4/createsequencedictionary/meta.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/gatk4/genomicsdbimport/environment.yml

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13 changes: 0 additions & 13 deletions modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff

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7 changes: 4 additions & 3 deletions modules/nf-core/gatk4/genomicsdbimport/main.nf

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18 changes: 5 additions & 13 deletions modules/nf-core/gatk4/genomicsdbimport/meta.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/gatk4/genotypegvcfs/environment.yml

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7 changes: 4 additions & 3 deletions modules/nf-core/gatk4/genotypegvcfs/main.nf

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9 changes: 5 additions & 4 deletions modules/nf-core/gatk4/genotypegvcfs/meta.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/gatk4/haplotypecaller/environment.yml

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17 changes: 9 additions & 8 deletions modules/nf-core/gatk4/haplotypecaller/main.nf

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33 changes: 29 additions & 4 deletions modules/nf-core/gatk4/haplotypecaller/meta.yml

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