diff --git a/.nf-core.yml b/.nf-core.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a4978789d27e9e96e75d1f534409692d9aef16e3
--- /dev/null
+++ b/.nf-core.yml
@@ -0,0 +1,3 @@
+repository_type: pipeline
+repository_type: pipeline
+repository_type: pipeline
diff --git a/modules.json b/modules.json
index 58d81058caad44803f3f87571bb8c15fbe880793..ef01adba6142fe35bf09a9bb4450705ff63138af 100644
--- a/modules.json
+++ b/modules.json
@@ -9,12 +9,6 @@
"bowtie2/build": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
- "cooler/cload": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
- "cooler/dump": {
- "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
- },
"cooler/zoomify": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
diff --git a/modules/nf-core/modules/cooler/cload/main.nf b/modules/local/cooler/cload.nf
similarity index 100%
rename from modules/nf-core/modules/cooler/cload/main.nf
rename to modules/local/cooler/cload.nf
diff --git a/modules/nf-core/modules/cooler/dump/main.nf b/modules/local/cooler/dump.nf
similarity index 100%
rename from modules/nf-core/modules/cooler/dump/main.nf
rename to modules/local/cooler/dump.nf
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index b020b70fc990b4b18ea44bdb14ab723bc95bc82b..f0a35fe0ed7d62bac50546002d6f3f747f037ded 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/modules/local/hicpro/bowtie2_merge.nf
@@ -1,7 +1,12 @@
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)
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index a137b78e44591fa897e516fe0351f8a324273868..00a88c8aec7666beddc1ef12cf7a7d3a9004de97 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -2,6 +2,8 @@ process COMBINE_MATES {
tag "$prefix"
label 'process_low'
+ conda (params.enable_conda ? "conda-forge::python=3.7.6 bioconda::pysam=0.15.4" : null)
+
input:
tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index 7b304e4dfc411f9a4066b05052c851af891a6b3d..63b08f2cfc276e5d1326317791fad8df60abda6c 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -1,7 +1,9 @@
process GET_RESTRICTION_FRAGMENTS {
tag "$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)
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index d8ea17f7541aceea09d677cae49e0843d550b13a..1d271a4087ff86a9bab2266447c2f6c27bbfd520 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -1,7 +1,9 @@
process GET_VALID_INTERACTION {
tag "$meta.id"
label 'process_low'
-
+
+ conda (params.enable_conda ? "conda-forge::python=3.7.6 bioconda::pysam=0.15.4" : null)
+
input:
tuple val(meta), path(bam)
path(resfrag)
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index 4bb40b8f1e5f081acd0044bd2bb78ef2561a01cf..c43bf3f1f3c51b084170f3680aa3313efcb3e70c 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/modules/local/hicpro/get_valid_interaction_dnase.nf
@@ -1,7 +1,9 @@
process GET_VALID_INTERACTION_DNASE {
tag "$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)
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index 99e4a6bd18ff61b674873b5053808b7297de17b4..305bc8713667048d79b76342b2071068c421994a 100644
--- a/modules/local/hicpro/hicpro2pairs.nf
+++ b/modules/local/hicpro/hicpro2pairs.nf
@@ -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
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index 8fb0eee32cca429b749d0d5f4394fbba36065c3e..c79afbcc3ecbb8eb1e89248fb03c9a8ce0c0b7d2 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -1,6 +1,8 @@
process MERGE_STATS {
label 'process_low'
+ conda (params.enable_conda ? "conda-forge::python=3.7.6" : null)
+
input:
tuple val(meta), path(fstat)
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index 7b4ee63a7cdc38059eb38a804cb17262dbf120db..ef7da6546cd1e903c6334a109e46bfe292146166 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -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)
diff --git a/modules/nf-core/modules/cooler/cload/meta.yml b/modules/nf-core/modules/cooler/cload/meta.yml
deleted file mode 100644
index ddb0443b23f7795c3db92c252e227babb10a7aeb..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/cooler/cload/meta.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-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"
diff --git a/modules/nf-core/modules/cooler/dump/main.nf~ b/modules/nf-core/modules/cooler/dump/main.nf~
deleted file mode 100644
index ffa36a1aaef96618328ecf280bebdab739625694..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/cooler/dump/main.nf~
+++ /dev/null
@@ -1,35 +0,0 @@
-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
- """
-}
diff --git a/modules/nf-core/modules/cooler/dump/meta.yml b/modules/nf-core/modules/cooler/dump/meta.yml
deleted file mode 100644
index fc12cdf3f5b4faf8107dd68852240ba25aeade28..0000000000000000000000000000000000000000
--- a/modules/nf-core/modules/cooler/dump/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-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"
diff --git a/subworkflows/local/cooler.nf b/subworkflows/local/cooler.nf
index 7e49aa423775be48da82fbbda4a5f93adf5013a4..8780b821d05b059f439cb17ea703a64ef581daf5 100644
--- a/subworkflows/local/cooler.nf
+++ b/subworkflows/local/cooler.nf
@@ -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 = [:]