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/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)