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Commit 6347311a authored by nservant's avatar nservant
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[MODIF] update

parent 60f80c27
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with 33 additions and 144 deletions
repository_type: pipeline
repository_type: pipeline
repository_type: pipeline
......@@ -9,12 +9,6 @@
"bowtie2/build": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"cooler/cload": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"cooler/dump": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"cooler/zoomify": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
......
process MERGE_BOWTIE2{
tag "$prefix"
label 'process_medium'
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(bam1), path(bam2)
......
......@@ -2,6 +2,8 @@ process COMBINE_MATES {
tag "$prefix"
label 'process_low'
conda (params.enable_conda ? "conda-forge::python=3.7.6 bioconda::pysam=0.15.4" : null)
input:
tuple val(meta), path(bam)
......
process GET_RESTRICTION_FRAGMENTS {
tag "$res_site"
label 'process_low'
conda (params.enable_conda ? "conda-forge::python=3.7.6 conda-forge::numpy=1.18.1" : null)
input:
path fasta
val(res_site)
......
process GET_VALID_INTERACTION {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::python=3.7.6 bioconda::pysam=0.15.4" : null)
input:
tuple val(meta), path(bam)
path(resfrag)
......
process GET_VALID_INTERACTION_DNASE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::python=3.7.6 bioconda::pysam=0.15.4" : null)
input:
tuple val(meta), path(bam)
......
......@@ -2,6 +2,11 @@ process HICPRO2PAIRS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
input:
tuple val(meta), path(vpairs)
path chrsize
......
process MERGE_STATS {
label 'process_low'
conda (params.enable_conda ? "conda-forge::python=3.7.6" : null)
input:
tuple val(meta), path(fstat)
......
......@@ -2,6 +2,8 @@ process ICE_NORMALIZATION{
tag "$rmaps"
label 'process_highmem'
conda (params.enable_conda ? "conda-forge::python=3.7.6 bioconda::iced=0.5.6" : null)
input:
tuple val(meta), val(res), path(rmaps), path(bed)
......
name: cooler_cload
description: Create a cooler from genomic pairs and bins
keywords:
- cool
tools:
- cooler:
description: Sparse binary format for genomic interaction matrices
homepage: https://cooler.readthedocs.io/en/latest/index.html
documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540"
licence: ["BSD-3-clause"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- pairs:
type: file
description: Path to contacts (i.e. read pairs) file.
- index:
type: file
description: Path to index file of the contacts.
- cool_bin:
type: value
description: Bins size in bp
- chromsizes:
type: file
description: Path to a chromsizes file.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "versions.yml"
- cool:
type: file
description: Output COOL file path
pattern: "*.cool"
- cool_bin:
type: value
description: Bins size in bp
authors:
- "@jianhong"
process COOLER_DUMP {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), val(resolution), path(cool)
output:
tuple val(meta), path("*.bedpe"), emit: bedpe
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${cool.baseName}"
def suffix = resolution ? "::$resolution" : ""
"""
cooler dump \\
$args \\
-o ${prefix}.bedpe \\
$cool$suffix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
END_VERSIONS
"""
}
name: cooler_dump
description: Dump a cooler’s data to a text stream.
keywords:
- dump
tools:
- cooler:
description: Sparse binary format for genomic interaction matrices
homepage: https://cooler.readthedocs.io/en/latest/index.html
documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540"
licence: ["BSD-3-Clause"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cool:
type: file
description: Path to COOL file
pattern: "*.{cool,mcool}"
- resolution:
type: value
description: Resolution
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bedpe:
type: file
description: Output text file
pattern: "*.bedpe"
authors:
- "@jianhong"
......@@ -4,14 +4,15 @@
* OUTPUT : cooler files
*/
include { COOLER_CLOAD } from '../../modules/nf-core/modules/cooler/cload/main'
include { COOLER_DUMP } from '../../modules/nf-core/modules/cooler/dump/main'
include { COOLER_ZOOMIFY } from '../../modules/nf-core/modules/cooler/zoomify/main'
include { COOLER_DUMP } from '../../modules/local/cooler/dump'
include { COOLER_CLOAD } from '../../modules/local/cooler/cload'
include { COOLER_BALANCE } from '../../modules/local/cooler/balance'
include { SPLIT_COOLER_DUMP } from '../../modules/local/split_cooler_dump'
include { COOLER_MAKEBINS } from '../../modules/local/cooler/makebins'
include { SPLIT_COOLER_DUMP } from '../../modules/local/split_cooler_dump'
// add resolution in meta
def addResolution(row) {
def meta = [:]
......
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