diff --git a/bin/mapped_2hic_dnase.py b/bin/mapped_2hic_dnase.py
index ff593666f03c5b82928ced06b941be296d6169ea..c417907a4483bd33bc6a6e0ceeb752d5c3d32121 100755
--- a/bin/mapped_2hic_dnase.py
+++ b/bin/mapped_2hic_dnase.py
@@ -362,7 +362,6 @@ if __name__ == "__main__":
if cur_handler is not None:
if not r1.is_unmapped and not r2.is_unmapped:
-
##reorient reads to ease duplicates removal
or1, or2 = get_ordered_reads(r1, r2)
or1_chrom = samfile.get_reference_name(or1.reference_id)
diff --git a/bin/mapped_2hic_fragments.py b/bin/mapped_2hic_fragments.py
index cc0e40b472dfb764ba1bf2f550c00c79bce7bd3f..a1298716ce83c4e99931534357c03634fd5d8301 100755
--- a/bin/mapped_2hic_fragments.py
+++ b/bin/mapped_2hic_fragments.py
@@ -619,7 +619,6 @@ if __name__ == "__main__":
r2_chrom = None
if r1_resfrag is not None or r2_resfrag is not None:
-
interactionType = get_interaction_type(r1, r1_chrom, r1_resfrag, r2, r2_chrom, r2_resfrag, verbose)
dist = get_PE_fragment_size(r1, r2, r1_resfrag, r2_resfrag, interactionType)
cdist = get_cis_dist(r1, r2)
diff --git a/bin/mergeSAM.py b/bin/mergeSAM.py
index 82ab8c34d979240d12de57b1f2510a54a79d2ca9..d670ec2c6a94b89035ab417b4146806099c2c5aa 100755
--- a/bin/mergeSAM.py
+++ b/bin/mergeSAM.py
@@ -71,7 +71,6 @@ def get_read_name(read):
def sam_flag(read1, read2, hr1, hr2):
-
f1 = read1.flag
f2 = read2.flag
diff --git a/modules.json b/modules.json
index 45540ca9ea0c4c8493525e58d8671176087348dc..6d7a0306685215f83fe5c69f51f6f54c1927fa04 100644
--- a/modules.json
+++ b/modules.json
@@ -7,52 +7,52 @@
"nf-core": {
"bowtie2/align": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"bowtie2/build": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cooler/balance": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cooler/cload": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cooler/dump": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cooler/makebins": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cooler/zoomify": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
}
}
diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf
index feaa30007099cae34a18eaa8105a3367e260e1b6..873bd243cd02102f327cba853197d39bc0ea860e 100644
--- a/modules/local/cooltools/eigscis.nf
+++ b/modules/local/cooltools/eigscis.nf
@@ -9,7 +9,7 @@ process COOLTOOLS_EIGSCIS {
conda "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
- 'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
+ 'biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
input:
tuple val(meta), path(cool), val(resolution)
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index 8a9127ea47824f9541c4faf2263d8e61030468c3..af53529ef80baa12dbd81bd0a2b8fa3ec2122cfa 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -9,7 +9,7 @@ process COOLTOOLS_INSULATION {
conda "bioconda::cooltools=0.5.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
- 'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
+ 'biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
input:
tuple val(meta), path(cool)
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index b6cae335c22111407b3d782e95a067ed087645e0..d86dc837e29e56aa4ba88cd2c66962444046647b 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -8,7 +8,7 @@ process HIC_FIND_TADS {
conda "bioconda::hicexplorer=3.7.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
- 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+ 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(cool)
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index 3e37d3fe7b466dbe45b2f19c220e2f9a65a07a9a..1143a05d3767ba4a9289e6f423cb7dc768d3d197 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
@@ -9,7 +9,7 @@ process HIC_PLOT_DIST_VS_COUNTS {
conda "bioconda::hicexplorer=3.7.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
- 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+ 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(cool)
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index 7a4e96be9aaf2470a10ca19672591e0f84853602..64aa6e6c05fd9e729ac26a0704f33b802f7dbb0c 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/modules/local/hicpro/bowtie2_merge.nf
@@ -5,7 +5,7 @@ process MERGE_BOWTIE2{
conda "bioconda::samtools=1.15.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
- 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+ 'biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(bam1), path(bam2)
diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf
index fd633a984f26b4cccc901a92e983cf0acfaa8eed..34b27aab498c8e1c45355d01b991d5900a619f33 100644
--- a/modules/local/hicpro/build_contact_maps.nf
+++ b/modules/local/hicpro/build_contact_maps.nf
@@ -5,15 +5,15 @@ process BUILD_CONTACT_MAPS{
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'quay.io/nf-core/ubuntu:20.04' }"
input:
- tuple val(meta), path(vpairs), val(resolution)
- tuple val(meta2), path(chrsize)
+ tuple val(meta), path(vpairs), val(resolution)
+ tuple val(meta2), path(chrsize)
output:
tuple val(meta), val(resolution), path("*.matrix"), path("*.bed"), emit: maps
-
+
script:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index da95be819a03560d75db2bc80ab3e8b72bf774aa..b0d828e3200bcb00fb4b94dcb071091ae352b7f7 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -5,7 +5,7 @@ process COMBINE_MATES {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index 64cb0792e4d93dfcc1b1e7d0b5d50bf7e0b75c73..8e85113944f79dc0b155ee9be441b2badf5c0245 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/modules/local/hicpro/dnase_mapping_stats.nf
@@ -5,7 +5,7 @@ process MAPPING_STATS_DNASE {
conda "bioconda::samtools=1.15.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
- 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+ 'biocontainers/samtools:1.15.1--h1170115_0' }"
input:
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index affc2d986a339d239602c6e66ad6f0d50517505e..56cd74a24a7d5102aad25cbe7032e31e2c4a1452 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -5,7 +5,7 @@ process GET_RESTRICTION_FRAGMENTS {
conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), path(fasta)
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index cc148371e52e04e96ca8dc9461a46ce80216b85e..bebd42197471c214ce0cde63c88ea89224387e76 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index 142d0cbd4f042fb0106c7e0380515f7b54c79953..d62318f87feac914b8b07796792fa18e363eef7e 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/modules/local/hicpro/get_valid_interaction_dnase.nf
@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION_DNASE {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index 2ba2a901b62791e733900b24da4f244cd2fbaba7..eb9b86b5e4ca0ace6549fe0c33a9dd1f63aaf5f3 100644
--- a/modules/local/hicpro/hicpro2pairs.nf
+++ b/modules/local/hicpro/hicpro2pairs.nf
@@ -5,7 +5,7 @@ process HICPRO2PAIRS {
conda "bioconda::pairix=0.3.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
- 'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
+ 'biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
input:
tuple val(meta), path(vpairs)
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index b25dc8a13d2f18bc5ae05742c5f15d77fd19627d..d9c2aecb5b2eb5c7574e139f7ffbbf3c8d3289de 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -5,7 +5,7 @@ process MERGE_STATS {
conda "conda-forge::python=3.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), path(fstat)
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index 29e568a20997c0a313a87cf964f1f8c10327228b..25c437ef795882591b0f50fcf4a235f29dc60822 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/modules/local/hicpro/merge_valid_interaction.nf
@@ -5,7 +5,7 @@ process MERGE_VALID_INTERACTION {
conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'quay.io/nf-core/ubuntu:20.04' }"
input:
tuple val(meta), path(vpairs)
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index 0a435edcd0f2a82c93be2a1b9bd832a721c270cf..74c96dc828399461d725fc52752cf98337b5dc02 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -5,7 +5,7 @@ process ICE_NORMALIZATION{
conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), val(res), path(rmaps), path(bed)
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index 5a96df412ea89845583fc363eccf2df49ba9458d..b9f2ea47e8f2ac40ae3a8ec17f6e01d0e22401b3 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -5,7 +5,7 @@ process TRIM_READS {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'quay.io/nf-core/ubuntu:20.04' }"
input:
tuple val(meta), path(reads)
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 595dc94d0eebd849d217c25349e4bb253bee64b6..6f6bad458bb8d83962f1d5a1bc922caeb7d3d9f9 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -4,7 +4,7 @@ process MULTIQC {
conda "bioconda::multiqc=1.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+ 'biocontainers/multiqc:1.13--pyhdfd78af_0' }"
input:
path multiqc_config
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 1624dfafe6425f07bbd15daf3b2735ea1187c0ec..096c80b0bd37b9a40bbf61cdefa13007f58b0c5d 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK {
conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
- 'quay.io/biocontainers/python:3.8.3' }"
+ 'biocontainers/python:3.8.3' }"
input:
path samplesheet
diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf
index 8b9e45b31d304545ea62946f4c4e0eacb7860002..5e392c140a86e51925b1ce751a81868dda5268ef 100644
--- a/modules/local/split_cooler_dump.nf
+++ b/modules/local/split_cooler_dump.nf
@@ -5,7 +5,7 @@ process SPLIT_COOLER_DUMP {
conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'quay.io/nf-core/ubuntu:20.04' }"
input:
tuple val(meta), path(bedpe)
diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
index 3d851866a30b4f629881864516f0789f6cae9443..311a1505eccdd3825db6ad8652305cb445148ae3 100644
--- a/modules/nf-core/bowtie2/align/main.nf
+++ b/modules/nf-core/bowtie2/align/main.nf
@@ -5,7 +5,7 @@ process BOWTIE2_ALIGN {
conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
- 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
+ 'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
input:
tuple val(meta) , path(reads)
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 551893af3b3bb1a3955f1cc7c0b50735c6fded8d..566a4accda99ed7c9c56564f6c3348bec439df11 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
conda "bioconda::bowtie2=2.4.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
- 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
+ 'biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
input:
tuple val(meta), path(fasta)
diff --git a/modules/nf-core/cooler/balance/main.nf b/modules/nf-core/cooler/balance/main.nf
index 4173a3c1291df7e25e3529d9ab8f2b6f8d1240b7..6e131d5b4717de6a6e7079b067154f7dd7e4e937 100644
--- a/modules/nf-core/cooler/balance/main.nf
+++ b/modules/nf-core/cooler/balance/main.nf
@@ -5,7 +5,7 @@ process COOLER_BALANCE {
conda "bioconda::cooler=0.8.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0':
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(cool), val(resolution)
diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf
index 80d61f07336f81233a6bd8ffb116e5a25e57048d..80109d48f449af278016bbda6cd08c46bbf8e183 100644
--- a/modules/nf-core/cooler/cload/main.nf
+++ b/modules/nf-core/cooler/cload/main.nf
@@ -5,7 +5,7 @@ process COOLER_CLOAD {
conda "bioconda::cooler=0.8.11"
container "${ 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' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(pairs), path(index), val(cool_bin)
diff --git a/modules/nf-core/cooler/dump/main.nf b/modules/nf-core/cooler/dump/main.nf
index b46c78cf35ec6b40276e2d792635f97b9909ab55..fed7502f8cb6a788b056c87aab3a2e71d26dd400 100644
--- a/modules/nf-core/cooler/dump/main.nf
+++ b/modules/nf-core/cooler/dump/main.nf
@@ -5,7 +5,7 @@ process COOLER_DUMP {
conda "bioconda::cooler=0.8.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(cool), val(resolution)
diff --git a/modules/nf-core/cooler/makebins/main.nf b/modules/nf-core/cooler/makebins/main.nf
index 7f0826197e99e9e79107359a8c65d7d60346dc49..25d6a40f636257c90251893c74eb2769200b41c1 100644
--- a/modules/nf-core/cooler/makebins/main.nf
+++ b/modules/nf-core/cooler/makebins/main.nf
@@ -5,7 +5,7 @@ process COOLER_MAKEBINS {
conda "bioconda::cooler=0.8.11"
container "${ 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' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(chromsizes), val(cool_bin)
diff --git a/modules/nf-core/cooler/zoomify/main.nf b/modules/nf-core/cooler/zoomify/main.nf
index f1cd8df79d02b8630c31de0620521cef0cdd6df0..95e7daff0d19429507d01033eb78eba491625220 100644
--- a/modules/nf-core/cooler/zoomify/main.nf
+++ b/modules/nf-core/cooler/zoomify/main.nf
@@ -5,7 +5,7 @@ process COOLER_ZOOMIFY {
conda "bioconda::cooler=0.8.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(cool)
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 3df21765b90921413962c3bb5ca44d117d829297..ebc8727339b0ee4ce7e2feb981a0aaf416723b57 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
label 'process_single'
// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
- conda "bioconda::multiqc=1.13"
+ conda "bioconda::multiqc=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+ 'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
index 60b546a012c457b5459490e732e6ac9be6979db1..c32657de7a2c09e82da1e753a234300fb76237ed 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
@@ -1,7 +1,9 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: custom_dumpsoftwareversions
description: Custom module used to dump software versions within the nf-core pipeline template
keywords:
- custom
+ - dump
- version
tools:
- custom:
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index b83b32c4d4242764a439f4d51e0255711f9cd40f..da03340857c4c90957c79c9f892030bc1bb397a3 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -3,10 +3,10 @@
"""Provide functions to merge multiple versions.yml files."""
-import platform
-from textwrap import dedent
import yaml
+import platform
+from textwrap import dedent
def _make_versions_html(versions):
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
index 580f87feade7280bb8d520551aa61f0021b3b88d..060a2e88527af75fabb1d87858c2885b6ca09547 100644
--- a/modules/nf-core/custom/getchromsizes/main.nf
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_GETCHROMSIZES {
conda "bioconda::samtools=1.16.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
- 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
+ 'biocontainers/samtools:1.16.1--h6899075_1' }"
input:
tuple val(meta), path(fasta)
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9ae5838158b28d2ae49270133fbbfe0ea673e991..07d5e433128b416714860fe1dca659219ba1d1ad 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -5,7 +5,7 @@ process FASTQC {
conda "bioconda::fastqc=0.11.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
- 'quay.io/biocontainers/fastqc:0.11.9--0' }"
+ 'biocontainers/fastqc:0.11.9--0' }"
input:
tuple val(meta), path(reads)
diff --git a/nextflow.config b/nextflow.config
index 9313b6a2312b28821180d9f3a38595d9b1312994..40507dd642c9a0dcd4fba6320ed5e750e1152445 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -54,13 +54,13 @@ params {
ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC'
}
}
-
+
min_restriction_fragment_size = 0
max_restriction_fragment_size = 0
min_insert_size = 0
max_insert_size = 0
save_pairs_intermediates = false
-
+
// Dnase Hi-C
dnase = false
min_cis_dist = 0
@@ -111,7 +111,7 @@ params {
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,digest'
-
+
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
@@ -242,6 +242,12 @@ env {
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
+// Set default registry for Docker and Podman independent of -profile
+// Will not be used unless Docker / Podman are enabled
+// Set to your registry if you have a mirror of containers
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true