From b607dc0eee8ef8b98fdc9fb151ca75b4c1d88c4c Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Fri, 2 Jun 2023 16:45:26 +0200
Subject: [PATCH] TO FIX markduplicates picard
---
conf/hicstuff.config | 22 ++++++
.../custom/{ => gatk4}/markduplicates/main.nf | 0
.../{ => gatk4}/markduplicates/meta.yml | 0
.../custom/picard/markduplicates/main.nf | 59 +++++++++++++++
.../custom/picard/markduplicates/meta.yml | 71 +++++++++++++++++++
.../nf-core/custom/samtools_n/sort/main.nf | 49 +++++++++++++
.../nf-core/custom/samtools_n/sort/meta.yml | 48 +++++++++++++
subworkflows/local/hicstuff_sub.nf | 34 +++++++--
8 files changed, 277 insertions(+), 6 deletions(-)
rename modules/nf-core/custom/{ => gatk4}/markduplicates/main.nf (100%)
rename modules/nf-core/custom/{ => gatk4}/markduplicates/meta.yml (100%)
create mode 100644 modules/nf-core/custom/picard/markduplicates/main.nf
create mode 100644 modules/nf-core/custom/picard/markduplicates/meta.yml
create mode 100644 modules/nf-core/custom/samtools_n/sort/main.nf
create mode 100644 modules/nf-core/custom/samtools_n/sort/meta.yml
diff --git a/conf/hicstuff.config b/conf/hicstuff.config
index 82360ec..3f5cdf6 100644
--- a/conf/hicstuff.config
+++ b/conf/hicstuff.config
@@ -245,6 +245,17 @@ process {
]
}
+ withName: 'PICARD_MARKDUPLICATES' {
+ ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
+ ext.args = { [
+ "--REMOVE_DUPLICATES true"
+ ].join('').trim() }
+ publishDir = [
+ path: { "${params.outdir}/picard/bam" },
+ mode: 'copy'
+ ]
+ }
+
withName: 'SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}_sorted" }
ext.args = { [
@@ -252,6 +263,17 @@ process {
].join('').trim() }
}
+ withName: 'SAMTOOLS_SORT_N' {
+ ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}_nsorted" }
+ ext.args = { [
+ "-n"
+ ].join('').trim() }
+ publishDir = [
+ path: { "${params.outdir}/gatk4/bam" },
+ mode: 'copy'
+ ]
+ }
+
withName: 'SAMTOOLS_INDEX' {
ext.args = { [
""
diff --git a/modules/nf-core/custom/markduplicates/main.nf b/modules/nf-core/custom/gatk4/markduplicates/main.nf
similarity index 100%
rename from modules/nf-core/custom/markduplicates/main.nf
rename to modules/nf-core/custom/gatk4/markduplicates/main.nf
diff --git a/modules/nf-core/custom/markduplicates/meta.yml b/modules/nf-core/custom/gatk4/markduplicates/meta.yml
similarity index 100%
rename from modules/nf-core/custom/markduplicates/meta.yml
rename to modules/nf-core/custom/gatk4/markduplicates/meta.yml
diff --git a/modules/nf-core/custom/picard/markduplicates/main.nf b/modules/nf-core/custom/picard/markduplicates/main.nf
new file mode 100644
index 0000000..b89101b
--- /dev/null
+++ b/modules/nf-core/custom/picard/markduplicates/main.nf
@@ -0,0 +1,59 @@
+process PICARD_MARKDUPLICATES {
+ tag "$meta.id"
+ label 'process_medium'
+
+ conda "bioconda::picard=3.0.0"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
+ 'quay.io/biocontainers/picard:3.0.0--hdfd78af_1' }"
+
+ input:
+ tuple val(meta), path(bam)
+ tuple val(meta2), path(fasta)
+ tuple val(meta3), path(fai)
+
+ output:
+ tuple val(meta), path("*.bam") , emit: bam
+ tuple val(meta), path("*.bai") , optional:true, emit: bai
+ tuple val(meta), path("*.metrics.txt"), emit: metrics
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def avail_mem = 3072
+ if (!task.memory) {
+ log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+ } else {
+ avail_mem = (task.memory.mega*0.8).intValue()
+ }
+ """
+ picard \\
+ -Xmx${avail_mem}M \\
+ MarkDuplicates \\
+ $args \\
+ --INPUT $bam \\
+ --OUTPUT ${prefix}.bam \\
+ --REFERENCE_SEQUENCE $fasta \\
+ --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+ END_VERSIONS
+ """
+
+ stub:
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ touch ${prefix}.bam
+ touch ${prefix}.bam.bai
+ touch ${prefix}.MarkDuplicates.metrics.txt
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+ END_VERSIONS
+ """
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/picard/markduplicates/meta.yml b/modules/nf-core/custom/picard/markduplicates/meta.yml
new file mode 100644
index 0000000..e463328
--- /dev/null
+++ b/modules/nf-core/custom/picard/markduplicates/meta.yml
@@ -0,0 +1,71 @@
+name: picard_markduplicates
+description: Locate and tag duplicate reads in a BAM file
+keywords:
+ - markduplicates
+ - pcr
+ - duplicates
+ - bam
+ - sam
+ - cram
+tools:
+ - picard:
+ description: |
+ A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+ data and formats such as SAM/BAM/CRAM and VCF.
+ homepage: https://broadinstitute.github.io/picard/
+ documentation: https://broadinstitute.github.io/picard/
+ licence: ["MIT"]
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - bam:
+ type: file
+ description: BAM file
+ pattern: "*.{bam,cram,sam}"
+ - meta2:
+ type: map
+ description: |
+ Groovy Map containing reference information
+ e.g. [ id:'genome' ]
+ - fasta:
+ type: file
+ description: Reference genome fasta file
+ pattern: "*.{fasta,fa}"
+ - meta3:
+ type: map
+ description: |
+ Groovy Map containing reference information
+ e.g. [ id:'genome' ]
+ - fai:
+ type: file
+ description: Reference genome fasta index
+ pattern: "*.{fai}"
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - bam:
+ type: file
+ description: BAM file with duplicate reads marked/removed
+ pattern: "*.{bam}"
+ - bai:
+ type: file
+ description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag
+ pattern: "*.{bai}"
+ - metrics:
+ type: file
+ description: Duplicate metrics file generated by picard
+ pattern: "*.{metrics.txt}"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+authors:
+ - "@drpatelh"
+ - "@projectoriented"
+ - "@ramprasadn"
\ No newline at end of file
diff --git a/modules/nf-core/custom/samtools_n/sort/main.nf b/modules/nf-core/custom/samtools_n/sort/main.nf
new file mode 100644
index 0000000..59a6e2a
--- /dev/null
+++ b/modules/nf-core/custom/samtools_n/sort/main.nf
@@ -0,0 +1,49 @@
+process SAMTOOLS_SORT_N {
+ tag "$meta.id"
+ label 'process_high' //medium
+
+ conda "bioconda::samtools=1.17"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
+ 'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
+
+ input:
+ tuple val(meta), path(bam)
+
+ output:
+ tuple val(meta), path("*.bam"), emit: bam
+ tuple val(meta), path("*.csi"), emit: csi, optional: true
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def sort_memory = (task.memory.mega/task.cpus).intValue()
+ if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+ """
+ samtools sort \\
+ $args \\
+ -@ $task.cpus \\
+ -m ${sort_memory}M \\
+ -o ${prefix}.bam \\
+ -T $prefix \\
+ $bam
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ END_VERSIONS
+ """
+
+ stub:
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ touch ${prefix}.bam
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ END_VERSIONS
+ """
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/samtools_n/sort/meta.yml b/modules/nf-core/custom/samtools_n/sort/meta.yml
new file mode 100644
index 0000000..1587857
--- /dev/null
+++ b/modules/nf-core/custom/samtools_n/sort/meta.yml
@@ -0,0 +1,48 @@
+name: samtools_sort
+description: Sort SAM/BAM/CRAM file
+keywords:
+ - sort
+ - bam
+ - sam
+ - cram
+tools:
+ - samtools:
+ description: |
+ SAMtools is a set of utilities for interacting with and post-processing
+ short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+ These files are generated as output by short read aligners like BWA.
+ homepage: http://www.htslib.org/
+ documentation: http://www.htslib.org/doc/samtools.html
+ doi: 10.1093/bioinformatics/btp352
+ licence: ["MIT"]
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - bam:
+ type: file
+ description: BAM/CRAM/SAM file
+ pattern: "*.{bam,cram,sam}"
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - bam:
+ type: file
+ description: Sorted BAM/CRAM/SAM file
+ pattern: "*.{bam,cram,sam}"
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ - csi:
+ type: file
+ description: BAM index file (optional)
+ pattern: "*.csi"
+authors:
+ - "@drpatelh"
+ - "@ewels"
\ No newline at end of file
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index 71b0053..69f04de 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -8,9 +8,11 @@ include { BUILD_MATRIX_COOL_ALT } from '../../modules/local/hicstuff/build_matri
include { FILTER_EVENT } from '../../modules/local/hicstuff/filter_event'
include { DISTANCE_LAW } from '../../modules/local/hicstuff/distance_law'
include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr'
-include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/markduplicates/main'
+include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/gatk4/markduplicates/main'
include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
+include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
+include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/custom/picard/markduplicates/main'
// Paired-end to Single-end
def pairToSingle(row, mates) {
@@ -67,16 +69,36 @@ workflow HICSTUFF_SUB {
BOWTIE2_ALIGNMENT.out.bam
)
+/* GATK4_MARKDUPLICATES(
+ SAMTOOLS_SORT.out.bam,
+ fasta.map{ it[1] }.collect(),
+ index.map{ it[1] }.collect()
+ )
+
+ SAMTOOLS_SORT_N(
+ GATK4_MARKDUPLICATES.out.bam
+ )
+
SAMTOOLS_INDEX(
- SAMTOOLS_SORT.out.bam
+ SAMTOOLS_SORT_N.out.bam
)
+ */
- GATK4_MARKDUPLICATES(
+ PICARD_MARKDUPLICATES(
SAMTOOLS_SORT.out.bam,
- fasta.map{ it[1] }.collect(),
- index.map{ it[1] }.collect()
+ fasta.collect(),
+ index.collect()
+ )
+
+ SAMTOOLS_SORT_N(
+ PICARD_MARKDUPLICATES.out.bam
)
- GATK4_MARKDUPLICATES.out.bam.set{ ch_bam }
+
+ SAMTOOLS_INDEX(
+ SAMTOOLS_SORT_N.out.bam
+ )
+
+ SAMTOOLS_SORT_N.out.bam.set{ ch_bam }
}
else {
--
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