From 16ed196a939969e9a3d81e6c997ebe0af36571c8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 22 May 2023 17:41:39 +0100
Subject: [PATCH] Update all NF-Core modules to latest version which includes
no quay.io prefix
---
modules.json | 20 +++++++++----------
modules/nf-core/bowtie2/align/main.nf | 2 +-
modules/nf-core/bowtie2/build/main.nf | 2 +-
modules/nf-core/cooler/balance/main.nf | 2 +-
modules/nf-core/cooler/cload/main.nf | 2 +-
modules/nf-core/cooler/dump/main.nf | 2 +-
modules/nf-core/cooler/makebins/main.nf | 2 +-
modules/nf-core/cooler/zoomify/main.nf | 2 +-
.../custom/dumpsoftwareversions/main.nf | 6 +++---
.../custom/dumpsoftwareversions/meta.yml | 2 ++
.../templates/dumpsoftwareversions.py | 4 ++--
modules/nf-core/custom/getchromsizes/main.nf | 2 +-
modules/nf-core/fastqc/main.nf | 2 +-
13 files changed, 26 insertions(+), 24 deletions(-)
diff --git a/modules.json b/modules.json
index 45540ca..6d7a030 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 3d85186..311a150 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
- 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
+ 'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
input:
tuple val(meta) , path(reads)
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 551893a..566a4ac 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
conda "bioconda::bowtie2=2.4.4"
container "${ 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 4173a3c..6e131d5 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0':
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(cool), val(resolution)
diff --git a/modules/nf-core/cooler/cload/main.nf b/modules/nf-core/cooler/cload/main.nf
index 80d61f0..80109d4 100644
--- a/modules/nf-core/cooler/cload/main.nf
+++ b/modules/nf-core/cooler/cload/main.nf
@@ -5,7 +5,7 @@ process COOLER_CLOAD {
conda "bioconda::cooler=0.8.11"
container "${ 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 b46c78c..fed7502 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(cool), val(resolution)
diff --git a/modules/nf-core/cooler/makebins/main.nf b/modules/nf-core/cooler/makebins/main.nf
index 7f08261..25d6a40 100644
--- a/modules/nf-core/cooler/makebins/main.nf
+++ b/modules/nf-core/cooler/makebins/main.nf
@@ -5,7 +5,7 @@ process COOLER_MAKEBINS {
conda "bioconda::cooler=0.8.11"
container "${ 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 f1cd8df..95e7daf 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
- 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+ 'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
input:
tuple val(meta), path(cool)
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 3df2176..ebc8727 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
label 'process_single'
// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
- conda "bioconda::multiqc=1.13"
+ conda "bioconda::multiqc=1.14"
container "${ 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 60b546a..c32657d 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
@@ -1,7 +1,9 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: custom_dumpsoftwareversions
description: Custom module used to dump software versions within the nf-core pipeline template
keywords:
- custom
+ - dump
- version
tools:
- custom:
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index b83b32c..da03340 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -3,10 +3,10 @@
"""Provide functions to merge multiple versions.yml files."""
-import platform
-from textwrap import dedent
import yaml
+import platform
+from textwrap import dedent
def _make_versions_html(versions):
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
index 580f87f..060a2e8 100644
--- a/modules/nf-core/custom/getchromsizes/main.nf
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_GETCHROMSIZES {
conda "bioconda::samtools=1.16.1"
container "${ 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 9ae5838..07d5e43 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)
--
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