nf-core · itrujnara · Jul 3, 2025 · Jun 18, 2025 · Jun 18, 2025 · Jun 20, 2025
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -75,7 +75,7 @@ jobs:
       fail-fast: false
       matrix:
         shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
-        profile: [conda, docker, singularity]
+        profile: [docker, singularity] # TODO: add Conda profile back when conda tests are fixed
         isMain:
           - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         # Exclude conda and singularity on dev
@@ -100,6 +100,7 @@ jobs:
         uses: ./.github/actions/nf-test
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NFT_USING_CONDA: ${{ matrix.profile == 'conda' }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}

diff --git a/README.md b/README.md
@@ -41,6 +41,10 @@ Steps 3 and 4 can be skipped with `--skip_merge`.
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
+:::warning
+Due to an nf-test issue outside our control, the current version of the pipeline is not tested with Conda. Most functionality should work with Conda, but we cannot guarantee it. We will rectify this issue as soon as possible.
+:::
+
 First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv title="samplesheet_fasta.csv"

diff --git a/modules.json b/modules.json
@@ -12,12 +12,12 @@
                     },
                     "csvtk/concat": {
                         "branch": "master",
-                        "git_sha": "cfe2a24902bfdfe8132f11461ffda92d257f9f09",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "csvtk/join": {
                         "branch": "master",
-                        "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "diamond/cluster": {

diff --git a/modules/local/plot_orthologs.nf b/modules/local/plot_orthologs.nf
@@ -4,8 +4,8 @@ process PLOT_ORTHOLOGS {
 
     conda     "conda-forge::r-tidyverse=2.0.0 conda-forge::r-reshape2=1.4.4 conda-forge::r-ggvenndiagram=1.5.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/r-ggvenndiagram_r-reshape2_r-tidyverse:3941632557872dac' :
-        'community.wave.seqera.io/library/r-ggvenndiagram_r-reshape2_r-tidyverse:6ab82708ae578c26' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/241121c567b6ac13fb664276916cc15e5b21b773612e30debf1de3cafe64fd97/data' :
+        'community.wave.seqera.io/library/r-ggvenndiagram_r-reshape2_r-tidyverse:b2486480b5e4dea4' }"
 
     input:
     tuple val(meta), path(score_table)

diff --git a/modules/local/stats2csv.nf b/modules/local/stats2csv.nf
@@ -4,8 +4,8 @@ process STATS2CSV {
 
     conda "conda-forge::python=3.11.0 conda-forge::pyyaml=5.4.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-deac90960ddeb4d14fb31faf92c0652d613b3327:10b46d090d02e9e22e206db80d14e994267520c3-0' :
-        'biocontainers/mulled-v2-deac90960ddeb4d14fb31faf92c0652d613b3327:10b46d090d02e9e22e206db80d14e994267520c3-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0d2b6ac1ed316a98eca861b5fbb6d52e11fd960e331a4f356e1dff8e7b544e2a/data' :
+        'community.wave.seqera.io/library/python_pyyaml:1d8dd531b5ad400c' }"
 
     input:
     tuple val(meta), path(stats)

diff --git a/modules/nf-core/csvtk/concat/environment.yml b/modules/nf-core/csvtk/concat/environment.yml
diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf
diff --git a/modules/nf-core/csvtk/concat/meta.yml b/modules/nf-core/csvtk/concat/meta.yml
diff --git a/modules/nf-core/csvtk/concat/tests/main.nf.test b/modules/nf-core/csvtk/concat/tests/main.nf.test
diff --git a/modules/nf-core/csvtk/concat/tests/main.nf.test.snap b/modules/nf-core/csvtk/concat/tests/main.nf.test.snap
diff --git a/modules/nf-core/csvtk/concat/tests/tags.yml b/modules/nf-core/csvtk/concat/tests/tags.yml
diff --git a/modules/nf-core/csvtk/join/environment.yml b/modules/nf-core/csvtk/join/environment.yml
diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf
diff --git a/modules/nf-core/csvtk/join/meta.yml b/modules/nf-core/csvtk/join/meta.yml