├── .circleci └── config.yml ├── Dockerfile ├── LICENSE ├── README.md ├── Singularity ├── Singularity.v1.1 ├── Singularity.v1.2 └── Singularity.v1.3 ├── WESpipeline.png ├── WESpipeline.svg ├── alignment.nf ├── dag.html ├── dag.png ├── deploy.sh ├── environment.yml ├── nextflow.config └── nextflow_schema.json /.circleci/config.yml: -------------------------------------------------------------------------------- 1 | version: 2 2 | 3 | jobs: 4 | build: 5 | machine: true 6 | steps: 7 | - checkout 8 | - run: wget -qO- get.nextflow.io | bash ; chmod 755 nextflow ; sudo ln -s ~/project/nextflow /usr/local/bin/ ; sudo apt-get install graphviz 9 | - run: cd ~ && git clone --depth=1 https://github.com/iarcbioinfo/data_test.git 10 | - run: echo " docker.runOptions = '-u $(id -u):$(id -g)' " > ~/.nextflow/config 11 | - run: cd ~/project/ ; docker build -t iarcbioinfo/alignment-nf . 12 | - run: cd ; nextflow run ~/project/alignment.nf --help 13 | - run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_folder ~/data_test/FASTQ/ --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results_FASTQ/ --cpu 2 --mem 4 --bwa_mem "bwa mem" 14 | - run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_folder ~/data_test/BAM/ --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --cpu 2 --mem 4 --bwa_mem "bwa mem" -with-dag dag.png 15 | - run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_folder ~/data_test/BAM/ --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --cpu 2 --mem 4 -with-dag dag.png 16 | - run: cd ; echo -e "SM\tRG\tpair1\tpair2\nfile1\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz" > input.txt ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --cpu 2 --mem 4 17 | - run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4 18 | - run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input.txt --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000.vcf.gz --trim --adapterremoval_opt "--qualitymax 93" --cpu 2 --mem 4 --mem_BQSR 4 19 | - run: cd ; echo -e "SM\tRG\tpair1\tpair2\nfile1\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2\tRG1\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz\nfile2\tRG2\t$HOME/data_test/FASTQ/NA06984_T_1.fastq.gz\t$HOME/data_test/FASTQ/NA06984_T_2.fastq.gz" > input_multiplex.txt ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --cpu 2 --mem 4 20 | - run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4 -with-dag alignment-nf_dag.png 21 | - run: cd ; nextflow run ~/project/alignment.nf -with-docker iarcbioinfo/alignment-nf --input_file input_multiplex.txt --ref ~/data_test/REF/17_7572000-7591000.fasta --output_folder ~/results/ --recalibration --indel_vcf ~/data_test/REF/1000G_phase1.indels.17_7572000-7591000.sites.vcf.gz --snp_vcf ~/data_test/REF/dbsnp_138.17_7572000-7591000.vcf.gz --cpu 2 --mem 4 --mem_BQSR 4 -with-dag alignment-nf_dag.html 22 | - run: cd ; cp ~/results/nf-pipeline_info/alignment-nf_dag.html ~/project/dag.html 23 | - deploy: 24 | branch: [master, dev] 25 | command: chmod +x deploy.sh && ./deploy.sh -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | ################## BASE IMAGE ##################### 2 | FROM continuumio/miniconda3:4.7.12 3 | 4 | ################## METADATA ####################### 5 | 6 | ARG bwa_mem2_version=2.2.1 7 | 8 | 9 | LABEL base_image="continuumio/miniconda3" 10 | LABEL version="4.7.12" 11 | LABEL software="alignment-nf" 12 | LABEL software.version="1.3" 13 | LABEL about.summary="Container image containing all requirements for alignment-nf" 14 | LABEL about.home="http://github.com/IARCbioinfo/alignment-nf" 15 | LABEL about.documentation="http://github.com/IARCbioinfo/alignment-nf/README.md" 16 | LABEL about.license_file="http://github.com/IARCbioinfo/alignment-nf/LICENSE.txt" 17 | LABEL about.license="GNU-3.0" 18 | 19 | 20 | ################## MAINTAINER ###################### 21 | MAINTAINER **nalcala** <**alcalan@fellows.iarc.fr**> 22 | 23 | 24 | ################## INSTALLATION ###################### 25 | COPY environment.yml / 26 | RUN apt-get --allow-releaseinfo-change update && apt-get install -y procps && apt-get clean -y 27 | RUN conda config --set channel_priority strict 28 | RUN conda env create -n alignment-nf -f /environment.yml && conda clean -a 29 | RUN ln -s /opt/conda/pkgs/bwakit-0.7.15-1/share/bwakit-0.7.15-1/k8 /usr/local/bin/. 30 | RUN wget -q https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-${bwa_mem2_version}_x64-linux.tar.bz2 && \ 31 | tar jxf bwa-mem2-${bwa_mem2_version}_x64-linux.tar.bz2 && \ 32 | mv bwa-mem2-${bwa_mem2_version}_x64-linux/* /usr/local/bin/. && \ 33 | rm -rf bwa-mem2-${bwa_mem2_version} 34 | ENV PATH /opt/conda/envs/alignment-nf/bin:$PATH 35 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # alignment-nf 2 | 3 | ## Nextflow pipeline for BAM realignment or fastq alignment 4 | [![CircleCI](https://circleci.com/gh/IARCbioinfo/alignment-nf.svg?style=svg)](https://circleci.com/gh/IARCbioinfo/alignment-nf) 5 | [![Docker Hub](https://img.shields.io/badge/docker-ready-blue.svg)](https://hub.docker.com/r/iarcbioinfo/alignment-nf/) 6 | [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/4522) 7 | 8 | 9 | ![Workflow representation](WESpipeline.png?raw=true "Scheme of alignment/realignment Workflow") 10 | 11 | ## Description 12 | 13 | Nextflow pipeline to perform BAM realignment or fastq alignment and QC, with/without local indel realignment and base quality score recalibration. 14 | 15 | ## Dependencies 16 | 17 | 1. Nextflow : for common installation procedures see the [IARC-nf](https://github.com/IARCbioinfo/IARC-nf) repository. 18 | 19 | ### Basic fastq alignment 20 | 2. [*bwa2*](https://github.com/bwa-mem2/bwa-mem2) (default) or [*bwa*](https://github.com/lh3/bwa) 21 | 3. [*samblaster*](https://github.com/GregoryFaust/samblaster) 22 | 4. [*sambamba*](https://github.com/lomereiter/sambamba) 23 | 24 | ### BAM files realignment 25 | 5. [*samtools*](http://samtools.sourceforge.net/) 26 | 27 | ### Adapter sequence trimming 28 | 6. [*AdapterRemoval*](https://github.com/MikkelSchubert/adapterremoval) 29 | 30 | ### ALT contigs handling 31 | 7. the *k8* javascript execution shell (e.g., available in the [*bwakit*](https://sourceforge.net/projects/bio-bwa/files/bwakit/) archive); must be in the PATH 32 | 8. javascript bwa-postalt.js and the additional fasta reference *.alt* file from [*bwakit*](https://github.com/lh3/bwa/tree/master/bwakit) must be in the same directory as the reference genome file. 33 | 34 | ### QC 35 | 9. [Qualimap](http://qualimap.bioinfo.cipf.es). 36 | 10. [Multiqc](http://multiqc.info). 37 | 38 | ### Base quality score recalibration 39 | 11. [GATK4](https://software.broadinstitute.org/gatk/guide/quickstart); wrapper 'gatk' must be in the path 40 | 12. [GATK bundle](https://software.broadinstitute.org/gatk/download/bundle) VCF files with lists of indels and SNVs (recommended: Mills gold standard indels VCFs, dbsnp VCF), and corresponding tabix indexes (.tbi) 41 | 42 | **A conda receipe, and docker and singularity containers are available with all the tools needed to run the pipeline (see "Usage")** 43 | 44 | ## Input 45 | | Type | Description | 46 | |-----------|---------------| 47 | | --input_folder | a folder with fastq files or bam files | 48 | 49 | ## Parameters 50 | 51 | * #### Mandatory 52 | 53 | | Name | Example value | Description | 54 | |-----------|--------------|-------------| 55 | |--ref | hg19.fasta | genome reference with its index files (*.fai*, *.sa*, *.bwt*, *.ann*, *.amb*, *.pac*, and *.dict*; in the same directory) | 56 | 57 | * #### Optional 58 | 59 | | Name | Default value | Description | 60 | |-----------|--------------|-------------| 61 | |--input_file | null | Input file (comma-separated) with 4 columns: SM (sample name), RG (read group ID), pair1 (first fastq of the pair), and pair2 (second fastq of the pair). | 62 | |--output_folder | . | Output folder for aligned BAMs| 63 | |--cpu | 8 | number of CPUs | 64 | |--cpu\_BQSR | 2 | number of CPUs for GATK base quality score recalibration | 65 | |--mem | 32 | memory| 66 | |--mem\_BQSR | 10 | memory for GATK base quality score recalibration | 67 | |--RG | PL:ILLUMINA | sequencing information for aligned (for *bwa*)| 68 | |--fastq_ext | fastq.gz | extension of fastq files| 69 | |--suffix1 | \_1 | suffix for second element of read files pair| 70 | |--suffix2 | \_2 | suffix for second element of read files pair| 71 | |--bed | | bed file with interval list| 72 | |--snp_vcf | dbsnp.vcf | path to SNP VCF from GATK bundle (default : dbsnp.vcf) | 73 | |--indel_vcf | Mills_1000G_indels.vcf | path to indel VCF from GATK bundle (default : Mills_1000G_indels.vcf) | 74 | |--postaltjs | bwa-postalt.js" | path to postalignment javascript *bwa-postalt.js*| 75 | |--feature_file | null | Path to feature file for qualimap | 76 | |--multiqc_config | null | config yaml file for multiqc | 77 | |--adapterremoval_opt | null | Command line options for AdapterRemoval | 78 | |--bwa_mem | bwa-mem2 mem | bwa-mem command; use "bwa mem" to switch to regular bwa-mem (both are in the docker and singularity containers) | 79 | 80 | * #### Flags 81 | 82 | Flags are special parameters without value. 83 | 84 | | Name | Description | 85 | |-----------|-------------| 86 | | --help | print usage and optional parameters | 87 | |--trim | enable adapter sequence trimming| 88 | |--recalibration | perform quality score recalibration (GATK)| 89 | |--alt | enable alternative contig handling (for reference genome hg38)| 90 | |--bwa_option_M | Trigger the -M option in bwa and the corresponding compatibility option in samblaster (marks shorter split hits as secondary) | 91 | 92 | ## Usage 93 | To run the pipeline on a series of fastq or BAM files in folder *input* and a fasta reference file hg19.fasta, one can type: 94 | 95 | ```bash 96 | nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity --input_folder input/ --ref hg19.fasta --output_folder output 97 | ``` 98 | 99 | To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda). 100 | 101 | 102 | ### Use bwa-mem instead of bwa-mem2 103 | To use bwa-mem, one can type: 104 | 105 | ```bash 106 | nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity --input_folder input/ --ref hg19.fasta --output_folder output --bwa_mem "bwa mem" 107 | ``` 108 | 109 | ### Enable adapter trimming 110 | To use the adapter trimming step, you must add the ***--trim* option**, as well as satisfy the requirements above mentionned. For example: 111 | ```bash 112 | nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity --input_folder input/ --ref hg19.fasta --output_folder output --trim 113 | ``` 114 | 115 | ### Enable ALT mode 116 | To use the alternative contigs handling mode, you must provide the **path to an ALT aware genome reference** (e.g., hg38) AND add the ***--alt* option**, as well as satisfy the above-mentionned requirements. For example: 117 | ```bash 118 | nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity --input_folder input/ --ref hg19.fasta --output_folder output --postaltjs /user/bin/bwa-0.7.15/bwakit/bwa-postalt.js --alt 119 | ``` 120 | 121 | ### Enable base quality score recalibration 122 | To use the base quality score recalibration step, you must provide the **path to 2 GATK bundle VCF files** with lists of known snps and indels, respectively, AND add the ***--recalibration* option**, as well as satisfy the requirements above mentionned. For example: 123 | ```bash 124 | nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity --input_folder input/ --ref hg19.fasta --output_folder output --snp_vcf GATKbundle/dbsnp.vcf.gz --indel_vcf GATKbundle/Mills_1000G_indels.vcf.gz --recalibration 125 | ``` 126 | 127 | ## Output 128 | | Type | Description | 129 | |-----------|---------------| 130 | | BAM/ | folder with BAM and BAI files of alignments or realignments | 131 | | QC/BAM/multiqc_qualimap_flagstat_*report.html | multiQC report for qualimap and samtools flagstat (duplicates) | 132 | | QC/BAM/multiqc_qualimap_flagstat_*report_data | data used for the multiQC report | 133 | | QC/qualimap/file_BQSRecalibrated.stats.txt | qualimap summary file | 134 | | QC/qualimap/file_BQSRecalibrated/ | qualimap files | 135 | | QC/BAM/BQSR/ | GATK base quality score recalibration outputs (tables and pdf comparing scores before/after recalibration)| 136 | 137 | ## Directed Acyclic Graph 138 | [![DAG](dag.png)](http://htmlpreview.github.io/?https://github.com/IARCbioinfo/alignment-nf/blob/dev/dag.html) 139 | 140 | ## FAQ 141 | ### Why did Indel realignment disappear from version 1.0? 142 | Indel realignment was removed following new GATK best practices for pre-processing. 143 | 144 | ## Contributions 145 | 146 | | Name | Email | Description | 147 | |-----------|---------------|-----------------| 148 | | Nicolas Alcala* | AlcalaN@fellows.iarc.fr | Developer to contact for support | 149 | | Catherine Voegele | VoegeleC@iarc.fr | Tester | 150 | | Vincent Cahais | CahaisV@iarc.fr | Tester | 151 | | Alexis Robitaille | RobitailleA@students.iarc.fr | Tester | 152 | 153 | -------------------------------------------------------------------------------- /Singularity/Singularity.v1.1: -------------------------------------------------------------------------------- 1 | From:iarcbioinfo/alignment-nf:v1.1 2 | Bootstrap:docker 3 | 4 | %labels 5 | MAINTAINER **alcalan** <**alcalan@iarc.fr**> 6 | DESCRIPTION Container image containing all requirements for pipeline alignment-nf 7 | VERSION 1.1 8 | -------------------------------------------------------------------------------- /Singularity/Singularity.v1.2: -------------------------------------------------------------------------------- 1 | From:iarcbioinfo/alignment-nf:v1.2 2 | Bootstrap:docker 3 | 4 | %labels 5 | MAINTAINER **alcalan** <**alcalan@iarc.fr**> 6 | DESCRIPTION Container image containing all requirements for pipeline alignment-nf 7 | VERSION 1.2 8 | -------------------------------------------------------------------------------- /Singularity/Singularity.v1.3: -------------------------------------------------------------------------------- 1 | From:iarcbioinfo/alignment-nf:v1.3 2 | Bootstrap:docker 3 | 4 | %labels 5 | MAINTAINER **alcalan** <**alcalan@iarc.fr**> 6 | DESCRIPTION Container image containing all requirements for pipeline alignment-nf 7 | VERSION 1.3 8 | -------------------------------------------------------------------------------- /WESpipeline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IARCbioinfo/alignment-nf/8ef9e12a836225a7a974961f66aabd6d1851160d/WESpipeline.png -------------------------------------------------------------------------------- /alignment.nf: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env nextflow 2 | 3 | // Copyright (C) 2017 IARC/WHO 4 | 5 | // This program is free software: you can redistribute it and/or modify 6 | // it under the terms of the GNU General Public License as published by 7 | // the Free Software Foundation, either version 3 of the License, or 8 | // (at your option) any later version. 9 | 10 | // This program is distributed in the hope that it will be useful, 11 | // but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 | // GNU General Public License for more details. 14 | 15 | // You should have received a copy of the GNU General Public License 16 | // along with this program. If not, see . 17 | 18 | params.input_folder = null 19 | params.input_file = null 20 | params.ref = 'hg19.fasta' 21 | params.cpu = 8 22 | params.mem = 32 23 | params.RG = "PL:ILLUMINA" 24 | params.fastq_ext = "fastq.gz" 25 | params.suffix1 = "_1" 26 | params.suffix2 = "_2" 27 | params.output_folder = "." 28 | params.bed = "" 29 | params.snp_vcf = "dbsnp.vcf" 30 | params.indel_vcf = "Mills_1000G_indels.vcf" 31 | params.postaltjs = "NO_FILE" 32 | params.feature_file = 'NO_FILE' 33 | params.mem_BQSR = 10 34 | params.cpu_BQSR = 2 35 | params.multiqc_config = 'NO_FILE' 36 | params.adapterremoval_opt = "" 37 | params.bwa_mem = "bwa-mem2 mem" 38 | params.bwa_option_M = null 39 | params.recalibration = null 40 | params.help = null 41 | params.alt = null 42 | params.trim = null 43 | 44 | log.info "" 45 | log.info "--------------------------------------------------------" 46 | log.info " alignment-nf 1.3.0: alignment/realignment workflow for whole exome/whole genome sequencing " 47 | log.info "--------------------------------------------------------" 48 | log.info "Copyright (C) IARC/WHO" 49 | log.info "This program comes with ABSOLUTELY NO WARRANTY; for details see LICENSE" 50 | log.info "This is free software, and you are welcome to redistribute it" 51 | log.info "under certain conditions; see LICENSE for details." 52 | log.info "--------------------------------------------------------" 53 | log.info "" 54 | 55 | 56 | if (params.help) { 57 | log.info "--------------------------------------------------------" 58 | log.info " USAGE " 59 | log.info "--------------------------------------------------------" 60 | log.info '' 61 | log.info 'nextflow run iarcbioinfo/alignment.nf [-with-docker] --input_folder input/ --ref hg19.fasta [OPTIONS]' 62 | log.info '' 63 | log.info 'Mandatory arguments:' 64 | log.info '--input_folder FOLDER Folder containing BAM or fastq files to be aligned.' 65 | log.info '--ref FILE Reference fasta file (with index).' 66 | log.info "" 67 | log.info 'Optional arguments:' 68 | log.info '--input_file STRING Input file (comma-separated) with 4 columns:' 69 | log.info ' SM(sample name), RG (read_group_ID), pair1 (path to fastq pair 1), ' 70 | log.info ' and pair2 (path to fastq pair 2).' 71 | log.info '--output_folder STRING Output folder (default: .).' 72 | log.info '--cpu INTEGER Number of cpu used by bwa mem and sambamba (default: 8).' 73 | log.info '--mem INTEGER Size of memory used for alignment (in GB) (default: 32).' 74 | log.info '--RG STRING Samtools read group specification with "\t" between fields.' 75 | log.info ' e.g. --RG "PL:ILLUMINA\tDS:custom_read_group".' 76 | log.info ' Default: "PL:ILLUMINA".' 77 | log.info '--fastq_ext STRING Extension of fastq files (default: fastq.gz)' 78 | log.info '--suffix1 STRING Suffix of fastq files 1 (default : _1)' 79 | log.info '--suffix2 STRING Suffix of fastq files 2 (default : _2)' 80 | log.info '--bed STRING Bed file with interval list' 81 | log.info '--snp_vcf STRING Path to SNP VCF from GATK bundle (default: dbsnp.vcf)' 82 | log.info '--indel_vcf STRING Path to indel VCF from GATK bundle (default: Mills_1000G_indels.vcf)' 83 | log.info '--postaltjs STRING Path to postalignment javascript bwa-postalt.js' 84 | log.info '--feature_file STRING Path to feature file for qualimap (default: NO_FILE)' 85 | log.info '--mem_BQSR INTEGER Size of memory used for GATK BQSR (in GB) (default: 10)' 86 | log.info '--cpu_BQSR INTEGER Number of cpu used by GATK BQSR (default: 2)' 87 | log.info '--multiqc_config STRING Config yaml file for multiqc (default : none)' 88 | log.info '--adapterremoval_opt STRING Command line options for AdapterRemoval (default : none)' 89 | log.info '--bwa_mem STRING bwa-mem command (default: "bwa-mem2 mem", alternative is "bwa mem")' 90 | log.info "" 91 | log.info "Flags:" 92 | log.info '--trim Enable adapter sequence trimming' 93 | log.info '--recalibration Performs base quality score recalibration (GATK)' 94 | log.info '--alt Enable alternative contig handling (for reference genome hg38)' 95 | log.info '--bwa_option_M Trigger the -M option in bwa and the corresponding compatibility option in samblaster' 96 | log.info '' 97 | exit 0 98 | }else { 99 | /* Software information */ 100 | log.info "input_folder=${params.input_folder}" 101 | log.info "input_file=${params.input_file}" 102 | log.info "ref=${params.ref}" 103 | log.info "cpu=${params.cpu}" 104 | log.info "mem=${params.mem}" 105 | log.info "RG=${params.RG}" 106 | log.info "fastq_ext=${params.fastq_ext}" 107 | log.info "suffix1= ${params.suffix1}" 108 | log.info "suffix2= ${params.suffix2}" 109 | log.info "output_folder=${params.output_folder}" 110 | log.info "bed=${params.bed}" 111 | log.info "snp_vcf=${params.snp_vcf}" 112 | log.info "indel_vcf=${params.indel_vcf}" 113 | log.info "postaltjs=${params.postaltjs}" 114 | log.info "feature_file=${params.feature_file}" 115 | log.info "mem_BQSR=${params.mem_BQSR}" 116 | log.info "cpu_BQSR=${params.cpu_BQSR}" 117 | log.info "multiqc_config=${params.multiqc_config}" 118 | log.info "bwa_mem=${params.bwa_mem}" 119 | log.info "adapterremoval_opt=${params.adapterremoval_opt}" 120 | log.info "recalibration=${params.recalibration}" 121 | log.info "alt=${params.alt}" 122 | log.info "trim=${params.trim}" 123 | log.info "bwa_option_M=${params.bwa_option_M}" 124 | log.info "help=${params.help}" 125 | } 126 | 127 | //multiqc config file 128 | ch_config_for_multiqc = file(params.multiqc_config) 129 | 130 | //read files 131 | ref = file(params.ref) 132 | ref_fai = file(params.ref+'.fai') 133 | ref_sa = file(params.ref+'.sa') 134 | ref_bwt = file(params.ref+'.bwt') 135 | ref_ann = file(params.ref+'.ann') 136 | ref_amb = file(params.ref+'.amb') 137 | ref_pac = file(params.ref+'.pac') 138 | ref_dict= file(params.ref.replaceFirst(/fasta/, "").replaceFirst(/fa/, "") +'dict') 139 | if(params.bwa_mem!="bwa-mem2 mem"){ 140 | ref_0123 = file('NO_0123') 141 | ref_bwt8bit = file('NO_bwt8bit') 142 | }else{ 143 | ref_0123 = file(params.ref+'.0123') 144 | ref_bwt8bit = file(params.ref+'.bwt.2bit.64') 145 | //ref_bwt8bit = file(params.ref+'.bwt.8bit.32') 146 | } 147 | //bwa-mem2 files 148 | if(params.alt){ 149 | ref_alt = file(params.ref+'.alt') 150 | }else{ 151 | ref_alt = file('NO_ALT') 152 | } 153 | postaltjs = file( params.postaltjs ) 154 | 155 | //get know site VCFs from GATK bundle 156 | known_snps = file( params.snp_vcf ) 157 | known_snps_index = file( params.snp_vcf+'.tbi' ) 158 | known_indels = file( params.indel_vcf ) 159 | known_indels_index = file( params.indel_vcf+'.tbi' ) 160 | 161 | //qualimap feature file 162 | qualimap_ff = file(params.feature_file) 163 | 164 | mode = 'fastq' 165 | if(params.input_file){ 166 | Channel.fromPath("${params.input_file}") 167 | .splitCsv(header: true, sep: '\t', strip: true) 168 | .map { row -> [row.SM , "_"+row.RG , file(row.pair1), file(row.pair2) ] } 169 | .into{readPairs0;readPairs4group} 170 | 171 | readPairsgrouped = readPairs4group.groupTuple(by: 0) 172 | .map{ a -> [a[0],a[1].size(),a[1],a[2],a[3]] } 173 | 174 | readPairs = readPairsgrouped.map{ a -> [a[0],a[1]] } 175 | .cross( readPairs0 ) 176 | .map{a -> [a[1][0],a[0][1],a[1][1],a[1][2],a[1][3] ] } 177 | }else{ 178 | if (file(params.input_folder).listFiles().findAll { it.name ==~ /.*${params.fastq_ext}/ }.size() > 0){ 179 | println "fastq files found, proceed with alignment" 180 | readPairs = Channel.fromFilePairs(params.input_folder +"/*{${params.suffix1},${params.suffix2}}" +'.'+ params.fastq_ext) 181 | .map { row -> [ row[0] , 1 , "" , row[1][0], row[1][1] ] } 182 | }else{ 183 | if (file(params.input_folder).listFiles().findAll { it.name ==~ /.*bam/ }.size() > 0){ 184 | println "BAM files found, proceed with realignment"; mode ='bam'; files = Channel.fromPath( params.input_folder+'/*.bam' ) 185 | }else{ 186 | println "ERROR: input folder contains no fastq nor BAM files"; System.exit(0) 187 | } 188 | } 189 | } 190 | 191 | if(mode=='bam'){ 192 | process bam_realignment { 193 | cpus params.cpu 194 | memory params.mem+'G' 195 | tag { file_tag } 196 | 197 | if(!params.recalibration) publishDir "${params.output_folder}/BAM/", mode: 'copy' 198 | 199 | input: 200 | file infile from files 201 | file ref 202 | file ref_sa 203 | file ref_bwt 204 | file ref_ann 205 | file ref_amb 206 | file ref_pac 207 | file ref_0123 208 | file ref_bwt8bit 209 | file ref_alt 210 | file postaltjs 211 | 212 | output: 213 | set val(file_tag), file("${file_tag_new}*.bam"), file("${file_tag_new}*.bai") into bam_bai_files 214 | 215 | shell: 216 | file_tag = infile.baseName 217 | file_tag_new=file_tag+'_realigned' 218 | if(params.trim) file_tag_new=file_tag_new+'_trimmed' 219 | if(params.alt) file_tag_new=file_tag_new+'_alt' 220 | 221 | if(params.alt==null){ 222 | ignorealt='-j' 223 | postalt='' 224 | }else{ 225 | ignorealt='' 226 | postalt='k8 bwa-postalt.js '+ref+'.alt |' 227 | } 228 | if(params.trim==null){ 229 | preproc='' 230 | }else{ 231 | preproc="AdapterRemoval ${params.adapterremoval_opt} --interleaved --file1 /dev/stdin --output1 /dev/stdout |" 232 | } 233 | if(params.bwa_option_M==null){ 234 | bwa_opt='' 235 | samblaster_opt='' 236 | }else{ 237 | bwa_opt='-M ' 238 | samblaster_opt='-M ' 239 | } 240 | bwa_threads = [params.cpu.intdiv(2) - 1,1].max() 241 | sort_threads = [params.cpu.intdiv(2) - 1,1].max() 242 | sort_mem = params.mem.div(4) 243 | ''' 244 | set -o pipefail 245 | samtools collate -uOn 128 !{file_tag}.bam tmp_!{file_tag} | samtools fastq - | !{preproc} !{params.bwa_mem} !{ignorealt} !{bwa_opt} -t!{bwa_threads} -R "@RG\\tID:!{file_tag}\\tSM:!{file_tag}\\t!{params.RG}" -p !{ref} - | !{postalt} samblaster !{samblaster_opt} --addMateTags --ignoreUnmated | sambamba view -S -f bam -l 0 /dev/stdin | sambamba sort -t !{sort_threads} -m !{sort_mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag_new}.bam /dev/stdin 246 | ''' 247 | } 248 | } 249 | if(mode!='bam'){ 250 | println "fastq mode" 251 | process fastq_alignment { 252 | cpus params.cpu 253 | memory params.mem+'GB' 254 | tag { "${file_tag}${read_group}" } 255 | 256 | input: 257 | set val(file_tag), val(nb_groups), val(read_group), file(pair1), file(pair2) from readPairs 258 | file ref 259 | file ref_fai 260 | file ref_sa 261 | file ref_bwt 262 | file ref_ann 263 | file ref_amb 264 | file ref_pac 265 | file ref_dict 266 | file ref_0123 267 | file ref_bwt8bit 268 | file ref_alt 269 | file postaltjs 270 | 271 | output: 272 | set val(file_tag), val(nb_groups), val(read_group), file("${file_tag_new}*.bam"), file("${file_tag_new}*.bai") into bam_bai_files0 273 | 274 | if(!params.recalibration & !params.input_file){ publishDir "${params.output_folder}/BAM/", mode: 'copy' } 275 | 276 | shell: 277 | file_tag_new=file_tag 278 | bwa_threads = [params.cpu.intdiv(2) - 1,1].max() 279 | sort_threads = [params.cpu.intdiv(2) - 1,1].max() 280 | sort_mem = [params.mem.intdiv(4),1].max() 281 | file_tag_new=file_tag_new+"${read_group}" 282 | if(params.trim) file_tag_new=file_tag_new+'_trimmed' 283 | if(params.alt) file_tag_new=file_tag_new+'_alt' 284 | if(params.alt==null){ 285 | ignorealt='-j' 286 | postalt='' 287 | }else{ 288 | ignorealt='' 289 | postalt='k8 bwa-postalt.js '+ref+'.alt |' 290 | } 291 | if(params.bwa_option_M==null){ 292 | bwa_opt='' 293 | samblaster_opt='' 294 | }else{ 295 | bwa_opt='-M ' 296 | samblaster_opt='-M ' 297 | } 298 | if(nb_groups > 1){ 299 | sort_opt=' -n' 300 | }else{ 301 | sort_opt='' 302 | } 303 | if(params.trim==null){ 304 | ''' 305 | set -o pipefail 306 | touch !{file_tag_new}.bam.bai 307 | !{params.bwa_mem} !{ignorealt} !{bwa_opt} -t!{bwa_threads} -R "@RG\\tID:!{file_tag}!{read_group}\\tSM:!{file_tag}\\t!{params.RG}" !{ref} !{pair1} !{pair2} | !{postalt} samblaster !{samblaster_opt} --addMateTags | sambamba view -S -f bam -l 0 /dev/stdin | sambamba sort !{sort_opt} -t !{sort_threads} -m !{sort_mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag_new}.bam /dev/stdin 308 | ''' 309 | }else{ 310 | ''' 311 | set -o pipefail 312 | touch !{file_tag_new}.bam.bai 313 | AdapterRemoval !{params.adapterremoval_opt} --file1 !{pair1} --file2 !{pair2} --interleaved-output --output1 /dev/stdout | !{params.bwa_mem} !{ignorealt} !{bwa_opt} -t!{bwa_threads} -R "@RG\\tID:!{file_tag}!{read_group}\\tSM:!{file_tag}\\t!{params.RG}" -p !{ref} - | !{postalt} samblaster !{samblaster_opt} --addMateTags | sambamba view -S -f bam -l 0 /dev/stdin | sambamba sort !{sort_opt} -t !{sort_threads} -m !{sort_mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag_new}.bam /dev/stdin 314 | ''' 315 | } 316 | } 317 | } 318 | 319 | if(mode!='bam'){ 320 | bam_bai_files0.into{bam_bai_2group;bam_bai_files2filter} 321 | bam_bai_grouped4merge = bam_bai_2group.groupTuple(by: 0) 322 | .map{ a -> [a[0],a[2].size(),a[2],a[3],a[4]] } 323 | 324 | bam_bai_files2filter.filter { a -> a[1] > 1 } 325 | .set{mult2QC} 326 | 327 | //QC on each run 328 | process qualimap_multi { 329 | cpus params.cpu 330 | memory params.mem+'G' 331 | tag { "${file_tag}${read_group}" } 332 | 333 | publishDir "${params.output_folder}/QC/BAM/qualimap/", mode: 'copy' 334 | 335 | input: 336 | set val(file_tag), val(nb_groups), val(read_group), file(bam), file(bai) from mult2QC 337 | file qff from qualimap_ff 338 | 339 | output: 340 | file ("${file_name}") into qualimap_multi_results 341 | file ("${file_name}.stats.txt") into flagstat_multi_results 342 | 343 | shell: 344 | feature = qff.name != 'NO_FILE' ? "--feature-file $qff" : '' 345 | file_name = bam.baseName 346 | ''' 347 | sambamba sort -t !{params.cpu} -m !{params.mem}G --tmpdir=!{file_name}_tmp -o !{file_name}_COsorted.bam !{bam} 348 | qualimap bamqc -nt !{params.cpu} !{feature} --skip-duplicated -bam !{file_name}_COsorted.bam --java-mem-size=!{params.mem}G -outdir !{file_name} -outformat html 349 | sambamba flagstat -t !{params.cpu} !{bam} > !{file_name}.stats.txt 350 | ''' 351 | } 352 | 353 | process multiqc_multi { 354 | cpus 2 355 | memory '1G' 356 | 357 | publishDir "${params.output_folder}/QC/BAM/qualimap", mode: 'copy' 358 | 359 | input: 360 | file qualimap_results from qualimap_multi_results.collect() 361 | file flagstat_results from flagstat_multi_results.collect() 362 | file multiqc_config from ch_config_for_multiqc 363 | 364 | output: 365 | file("*report.html") into multi_output 366 | file("multiqc_multiplex_qualimap_flagstat_report_data/") into multi_output_data 367 | 368 | shell: 369 | if( multiqc_config.name=='NO_FILE' ){ 370 | opt = "" 371 | }else{ 372 | opt = "--config ${multiqc_config}" 373 | } 374 | ''' 375 | multiqc . -n multiqc_multiplex_qualimap_flagstat_report.html !{opt} --comment "WGS/WES pre-merging QC report" 376 | ''' 377 | } 378 | 379 | process merge { 380 | cpus params.cpu 381 | memory params.mem+'G' 382 | tag { file_tag } 383 | if(!params.recalibration) publishDir "$params.output_folder/BAM/", mode: 'copy', pattern: "*.bam*" 384 | 385 | input: 386 | set val(file_tag), val(nb_groups), val(read_group), file(bams), file(bais) from bam_bai_grouped4merge 387 | 388 | output: 389 | set val(file_tag), file("${file_tag_new}.bam"), file("${file_tag_new}.bam.bai") into bam_bai_files 390 | 391 | shell: 392 | file_tag_new=file_tag 393 | for( rgtmp in read_group ){ 394 | file_tag_new=file_tag_new+"${rgtmp}" 395 | } 396 | if(params.trim) file_tag_new=file_tag_new+'_trimmed' 397 | if(params.alt) file_tag_new=file_tag_new+'_alt' 398 | if(nb_groups>1){ 399 | merge_threads = [params.cpu.intdiv(2) - 1,1].max() 400 | sort_threads = [params.cpu.intdiv(2) - 1,1].max() 401 | sort_mem = params.mem.div(2) 402 | bam_files=" " 403 | for( bam in bams ){ 404 | bam_files=bam_files+" ${bam}" 405 | } 406 | file_tag_new=file_tag_new+"_merged" 407 | if(params.bwa_option_M==null){ 408 | samblaster_opt='' 409 | }else{ 410 | samblaster_opt='-M ' 411 | } 412 | ''' 413 | sambamba merge -t !{merge_threads} -l 0 /dev/stdout !{bam_files} | sambamba view -h /dev/stdin | samblaster !{samblaster_opt} --addMateTags | sambamba view -S -f bam -l 0 /dev/stdin | sambamba sort -t !{sort_threads} -m !{sort_mem}G --tmpdir=!{file_tag}_tmp -o !{file_tag_new}.bam /dev/stdin 414 | ''' 415 | }else{ 416 | ''' 417 | touch nomerge 418 | ''' 419 | } 420 | } 421 | } 422 | 423 | if(params.recalibration){ 424 | println "BQSR" 425 | 426 | // base quality score recalibration 427 | process base_quality_score_recalibration { 428 | cpus params.cpu_BQSR 429 | memory params.mem_BQSR+'G' 430 | tag { file_tag } 431 | 432 | publishDir "$params.output_folder/BAM/", mode: 'copy', pattern: "*bam*" 433 | publishDir "$params.output_folder/QC/BAM/BQSR/", mode: 'copy', 434 | saveAs: {filename -> 435 | if (filename.indexOf("table") > 0) "$filename" 436 | else if (filename.indexOf("plots") > 0) "$filename" 437 | else null 438 | } 439 | 440 | input: 441 | set val(file_tag), file(bam), file(bai) from bam_bai_files 442 | file known_snps 443 | file known_snps_index 444 | file known_indels 445 | file known_indels_index 446 | file ref 447 | file ref_fai 448 | file ref_dict 449 | 450 | output: 451 | file("*_recal.table") into recal_table_files 452 | file("*plots.pdf") into recal_plots_files 453 | set val(file_tag), file("${file_tag_new}.bam"), file("${file_tag_new}.bam.bai") into final_bam_bai_files 454 | 455 | shell: 456 | file_name=bam.baseName 457 | file_tag_new=file_name+'_BQSRecalibrated' 458 | ''' 459 | gatk BaseRecalibrator --java-options "-Xmx!{params.mem_BQSR}G" -R !{ref} -I !{bam} --known-sites !{known_snps} --known-sites !{known_indels} -O !{file_name}_recal.table 460 | gatk ApplyBQSR --java-options "-Xmx!{params.mem_BQSR}G" -R !{ref} -I !{bam} --bqsr-recal-file !{file_name}_recal.table -O !{file_tag_new}.bam 461 | gatk BaseRecalibrator --java-options "-Xmx!{params.mem_BQSR}G" -R !{ref} -I !{file_tag_new}.bam --known-sites !{known_snps} --known-sites !{known_indels} -O !{file_tag_new}_recal.table 462 | gatk AnalyzeCovariates --java-options "-Xmx!{params.mem_BQSR}G" -before !{file_name}_recal.table -after !{file_tag_new}_recal.table -plots !{file_tag_new}_recalibration_plots.pdf 463 | mv !{file_tag_new}.bai !{file_tag_new}.bam.bai 464 | ''' 465 | } 466 | }else{ 467 | final_bam_bai_files = bam_bai_files 468 | recal_table_files = Channel.from ( 'NOFILE1', 'NOFILE2' ) 469 | } 470 | 471 | 472 | process qualimap_final { 473 | cpus params.cpu 474 | memory params.mem+'G' 475 | tag { file_tag } 476 | 477 | publishDir "${params.output_folder}/QC/BAM/qualimap/", mode: 'copy' 478 | 479 | input: 480 | set val(file_tag), file(bam), file(bai) from final_bam_bai_files 481 | file qff from qualimap_ff 482 | 483 | output: 484 | file ("${file_name}") into qualimap_results 485 | file ("${file_name}.stats.txt") into flagstat_results 486 | 487 | shell: 488 | feature = qff.name != 'NO_FILE' ? "--feature-file $qff" : '' 489 | file_name=bam.baseName 490 | ''' 491 | qualimap bamqc -nt !{params.cpu} !{feature} --skip-duplicated -bam !{bam} --java-mem-size=!{params.mem}G -outdir !{file_name} -outformat html 492 | sambamba flagstat -t !{params.cpu} !{bam} > !{file_name}.stats.txt 493 | ''' 494 | } 495 | 496 | process multiqc_final { 497 | cpus 2 498 | memory '2G' 499 | 500 | publishDir "${params.output_folder}/QC/BAM/", mode: 'copy' 501 | 502 | input: 503 | file qualimap_results from qualimap_results.collect() 504 | file flagstat_results from flagstat_results.collect() 505 | file BQSR_results from recal_table_files.collect() 506 | file multiqc_config from ch_config_for_multiqc 507 | 508 | output: 509 | file("*report.html") into final_output 510 | file("multiqc_qualimap_flagstat_BQSR_report_data/") into final_output_data 511 | 512 | shell: 513 | if( multiqc_config.name=='NO_FILE' ){ 514 | opt = "" 515 | }else{ 516 | opt = "--config ${multiqc_config}" 517 | } 518 | ''' 519 | multiqc . -n multiqc_qualimap_flagstat_BQSR_report.html !{opt} --comment "WGS/WES final QC report" 520 | ''' 521 | } 522 | -------------------------------------------------------------------------------- /dag.html: -------------------------------------------------------------------------------- 1 | 16 | 17 | 18 | 19 | 20 | Nextflow Cytoscape.js with Dagre 21 | 22 | 23 | 24 | 31 | 32 | 52 | 53 | 140 | 141 | 142 | 143 |

Nextflow Cytoscape.js with Dagre

144 |
145 | 146 | 147 | 148 | -------------------------------------------------------------------------------- /dag.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IARCbioinfo/alignment-nf/8ef9e12a836225a7a974961f66aabd6d1851160d/dag.png -------------------------------------------------------------------------------- /deploy.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | cd ~/project/ 3 | commitID=`git log -n 1 --pretty="%h" -- environment.yml` 4 | sed -i '/^# environment.yml/d' Singularity && echo -e "\n# environment.yml commit ID: $commitID\n" >> Singularity 5 | git config --global user.email "alcalan@fellows.iarc.fr" 6 | git config --global user.name "Circle CI_$CIRCLE_PROJECT_REPONAME_$CIRCLE_BRANCH" 7 | git add dag.png 8 | git add dag.html 9 | git status 10 | git commit -m "circle CI deployment [skip ci]" 11 | git push origin $CIRCLE_BRANCH 12 | 13 | curl -H "Content-Type: application/json" --data "{\"source_type\": \"Branch\", \"source_name\": \"$CIRCLE_BRANCH\"}" -X POST https://registry.hub.docker.com/u/iarcbioinfo/alignment-nf/trigger/5360932c-62ae-4969-9581-312f4089660e/ 14 | 15 | 16 | -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- 1 | name: alignment 2 | channels: 3 | - conda-forge 4 | - bioconda 5 | dependencies: 6 | - gatk4=4.1.7.0 7 | - multiqc=1.9 8 | - qualimap=2.2.2d 9 | - sambamba=0.7.1 10 | - samtools=1.9 11 | - samblaster=0.1.26 12 | - bwa=0.7.17 13 | - bwakit=0.7.15 14 | - r-data.table=1.12.8 15 | - r-dplyr=1.0.0 16 | - r-ggplot2=3.3.2 17 | - r-gplots=3.0.3 18 | - r-gsalib=2.1.0 19 | - adapterremoval=2.3.1 20 | -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- 1 | manifest { 2 | homePage = 'https://github.com/iarcbioinfo/alignment-nf' 3 | description = 'Align fastq or realign BAM files from Whole Exome/Whole Genome sequencing data' 4 | mainScript = 'alignment.nf' 5 | } 6 | 7 | profiles { 8 | conda { 9 | process.conda = "$baseDir/environment.yml" 10 | conda.createTimeout = "200 min" 11 | } 12 | docker { 13 | docker.enabled = true 14 | process.container = 'iarcbioinfo/alignment-nf:v1.3' 15 | } 16 | singularity { 17 | singularity.enabled = true 18 | process.container = 'shub://IARCbioinfo/alignment-nf:v1.3' 19 | pullTimeout = "200 min" 20 | } 21 | } 22 | 23 | process { 24 | shell = ['/bin/bash','-o','pipefail'] 25 | } 26 | 27 | params.output_folder="." 28 | 29 | 30 | timeline { 31 | enabled = true 32 | file = "${params.output_folder}/nf-pipeline_info/alignment-nf_timeline.html" 33 | } 34 | 35 | report { 36 | enabled = true 37 | file = "${params.output_folder}/nf-pipeline_info/alignment-nf_report.html" 38 | } 39 | 40 | trace { 41 | enabled = true 42 | file = "${params.output_folder}/nf-pipeline_info/alignment-nf_trace.txt" 43 | } 44 | 45 | dag { 46 | enabled = true 47 | file = "${params.output_folder}/nf-pipeline_info/alignment-nf_dag.html" 48 | } 49 | -------------------------------------------------------------------------------- /nextflow_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$schema": "http://json-schema.org/draft-07/schema", 3 | "$id": "https://raw.githubusercontent.com/IARCbioinfo/alignment-nf/master/nextflow_schema.json", 4 | "title": "IARCbioinfo alignment-nf pipeline parameters", 5 | "description": "This pipeline performs fastq alignment or BAM realignment", 6 | "type": "object", 7 | "definitions": { 8 | "input_output_params": { 9 | "title": "Input_output_params", 10 | "type": "object", 11 | "description": "Input and output parameters", 12 | "default": "", 13 | "properties": { 14 | "input_folder": { 15 | "type": "string", 16 | "description": "Folder containing BAM or fastq files to be aligned" 17 | }, 18 | "input_file": { 19 | "type": "string", 20 | "description": "Input file (comma-separated) with 4 columns: SM (sample name), RG (read group ID), pair1 (first fastq of the pair), and pair2 (second fastq of the pair)." 21 | }, 22 | "fastq_ext": { 23 | "type": "string", 24 | "description": "Extension of fastq files", 25 | "default": "fastq.gz" 26 | }, 27 | "suffix1": { 28 | "type": "string", 29 | "default": "_1", 30 | "description": "Suffix for 1st element of fastq read file pair" 31 | }, 32 | "suffix2": { 33 | "type": "string", 34 | "default": "_2", 35 | "description": "Suffix for 2nd element of fastq read file pair" 36 | }, 37 | "output_folder": { 38 | "type": "string", 39 | "description": "Output folder for aligned BAMs", 40 | "default": "." 41 | } 42 | } 43 | }, 44 | "computing_params": { 45 | "title": "Computing_params", 46 | "type": "object", 47 | "description": "Computing parameters", 48 | "default": "", 49 | "properties": { 50 | "cpu": { 51 | "type": "integer", 52 | "default": 8, 53 | "description": "Number of cpu used by bwa mem and sambamba" 54 | }, 55 | "cpu_BQSR": { 56 | "type": "integer", 57 | "description": "Number of CPUs used by GATK BQSR", 58 | "default": 2 59 | }, 60 | "mem": { 61 | "type": "integer", 62 | "description": "Size of memory used for alignment (in GB)", 63 | "default": 32 64 | }, 65 | "mem_BQSR": { 66 | "type": "integer", 67 | "description": "Size of memory used for GATK BQSR", 68 | "default": 10 69 | } 70 | } 71 | }, 72 | "ref_params": { 73 | "title": "Ref_params", 74 | "type": "object", 75 | "description": "Reference parameters", 76 | "default": "", 77 | "properties": { 78 | "ref": { 79 | "type": "string", 80 | "description": "Genome reference fasta file with its index files (.fai, .sa, .bwt, .ann, .amb, .pac, and .dict; in the same directory)", 81 | "default": "hg19.fasta" 82 | }, 83 | "bed": { 84 | "type": "string", 85 | "description": "Bed file with interval list" 86 | }, 87 | "snp_vcf": { 88 | "type": "string", 89 | "default": "dbsnp.vcf", 90 | "description": "Path to SNP VCF from GATK bundle" 91 | }, 92 | "indel_vcf": { 93 | "type": "string", 94 | "default": "Mills_1000G_indels.vcf", 95 | "description": "Path to indel VCF from GATK bundle" 96 | } 97 | } 98 | }, 99 | "pipeline_params": { 100 | "title": "Pipeline_params", 101 | "type": "object", 102 | "description": "Pipeline parameters", 103 | "default": "", 104 | "properties": { 105 | "RG": { 106 | "type": "string", 107 | "description": "Samtools read group specification with \"\\t\" between fields (for bwa)", 108 | "default": "PL:ILLUMINA" 109 | }, 110 | "postaltjs": { 111 | "type": "string", 112 | "default": "NO_FILE", 113 | "description": "Path to postalignment javascript bwa-postalt.js" 114 | }, 115 | "feature_file": { 116 | "type": "string", 117 | "description": "Path to feature file for qualimap", 118 | "default": "NO_FILE" 119 | }, 120 | "multiqc_config": { 121 | "type": "string", 122 | "description": "Config yaml file for multiqc", 123 | "default": "NO_FILE" 124 | }, 125 | "adapterremoval_opt": { 126 | "type": "string", 127 | "description": "Command line options for AdapterRemoval" 128 | }, 129 | "bwa_mem": { 130 | "type": "string", 131 | "description": "bwa-mem command", 132 | "default": "bwa-mem2 mem", 133 | "enum": [ 134 | "bwa-mem2 mem", 135 | "bwa mem" 136 | ] 137 | }, 138 | "trim": { 139 | "type": "boolean", 140 | "description": "Enable adapter sequence trimming" 141 | }, 142 | "recalibration": { 143 | "type": "boolean", 144 | "description": "Perform base quality score recalibration (GATK)" 145 | }, 146 | "alt": { 147 | "type": "boolean", 148 | "description": "Enable alternative contig handling (for reference genome hg38)" 149 | }, 150 | "bwa_option_M": { 151 | "type": "boolean", 152 | "description": "Trigger the -M option in bwa and the corresponding compatibility option in samblaster (marks shorter split hits as secondary)" 153 | }, 154 | "help": { 155 | "type": "boolean", 156 | "description": "Display help" 157 | } 158 | } 159 | } 160 | }, 161 | "allOf": [ 162 | { 163 | "$ref": "#/definitions/input_output_params" 164 | }, 165 | { 166 | "$ref": "#/definitions/computing_params" 167 | }, 168 | { 169 | "$ref": "#/definitions/ref_params" 170 | }, 171 | { 172 | "$ref": "#/definitions/pipeline_params" 173 | } 174 | ] 175 | } 176 | --------------------------------------------------------------------------------