nf-core · pinin4fjords · May 11, 2023 · May 11, 2023 · May 11, 2023 · May 11, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,11 +8,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [[#124](https://github.com/nf-core/differentialabundance/pull/124)] - Template update for nf-core/tools v2.8 ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jasmezz](https://github.com/jasmezz))
+- [[#129](https://github.com/nf-core/differentialabundance/pull/129)] - Module updates to fit with recent registry changes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse), [@adamrtalbot](https://github.com/adamrtalbot))
 
 ### `Fixed`
 
 - [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by [@nvnieuwk](https://github.com/nvnieuwk))
 - [[#122](https://github.com/nf-core/differentialabundance/pull/126)] - Add spaces to satisfy nf-core download for singularity ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
+- [[#127](https://github.com/nf-core/differentialabundance/issues/127)] - [Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv ([@ctuni](https://github.com/ctuni), review by [@pinin4fjords](https://github.com/pinin4fjords))
 
 ## v1.2.0 - 2023-04-19
 

diff --git a/modules.json b/modules.json
@@ -7,82 +7,82 @@
                 "nf-core": {
                     "affy/justrma": {
                         "branch": "master",
-                        "git_sha": "960cc23c7bb97ff718e162efeefdd842fa8f5c70",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "atlasgeneannotationmanipulation/gtf2featureannotation": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/matrixfilter": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/tabulartogseacls": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     },
                     "custom/tabulartogseagct": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     },
                     "deseq2/differential": {
                         "branch": "master",
-                        "git_sha": "e05db1b791ba8202853f275438fcc67c563ca479",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "gsea/gsea": {
                         "branch": "master",
-                        "git_sha": "595f49842df5f8791b1dac9f5feabb56813facc5",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     },
                     "limma/differential": {
                         "branch": "master",
-                        "git_sha": "4805d97c29f1a3cdfc26a828796296e2d58076e1",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "rmarkdownnotebook": {
                         "branch": "master",
-                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/app": {
                         "branch": "master",
-                        "git_sha": "7be616acb9436d748631011420d3c8f73c181cbe",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticdifferential": {
                         "branch": "master",
-                        "git_sha": "7be616acb9436d748631011420d3c8f73c181cbe",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticexploratory": {
                         "branch": "master",
-                        "git_sha": "7be616acb9436d748631011420d3c8f73c181cbe",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/validatefomcomponents": {
                         "branch": "master",
-                        "git_sha": "7be616acb9436d748631011420d3c8f73c181cbe",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "cc1f997fab6d8fde5dc0e6e2a310814df5b53ce7",
+                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/tabular_to_gsea_chip.nf b/modules/local/tabular_to_gsea_chip.nf
@@ -5,7 +5,7 @@ process TABULAR_TO_GSEA_CHIP {
     conda "conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'biocontainers/gawk:5.1.0' }"
 
     input:
     path tsv

diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf
diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/matrixfilter/main.nf b/modules/nf-core/custom/matrixfilter/main.nf
diff --git a/modules/nf-core/custom/tabulartogseacls/main.nf b/modules/nf-core/custom/tabulartogseacls/main.nf
diff --git a/modules/nf-core/custom/tabulartogseagct/main.nf b/modules/nf-core/custom/tabulartogseagct/main.nf
diff --git a/modules/nf-core/custom/tabulartogseagct/meta.yml b/modules/nf-core/custom/tabulartogseagct/meta.yml
diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf
diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf
diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf
diff --git a/modules/nf-core/rmarkdownnotebook/meta.yml b/modules/nf-core/rmarkdownnotebook/meta.yml
diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf
diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf
diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -238,7 +238,6 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        //docker.registry        = 'quay.io'
         docker.userEmulation   = true
         conda.enabled          = false
         singularity.enabled    = false
@@ -262,7 +261,6 @@ profiles {
     }
     podman {
         podman.enabled         = true
-        //podman.registry        = 'quay.io'
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -310,6 +308,11 @@ profiles {
     test_affy { includeConfig 'conf/test_affy.config' }
 }
 
+// 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'
 
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {