Add README to modules build with Docker (nf-core#4935)

* add Dockerfile * remove environment.yml * EC lint * add comment * remove Dockerfile * add README --------- Co-authored-by: Matthias De Smet <[email protected]>
alexnater · Mar 21, 2024 · 5671e5f · 5671e5f
1 parent f61dc22
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diff --git a/modules/nf-core/deepvariant/README.md b/modules/nf-core/deepvariant/README.md
@@ -0,0 +1,9 @@
+# Conda is not supported at the moment
+
+The [bioconda](https://bioconda.github.io/recipes/deepvariant/README.html) recipe is not fully working as expected
+
+Hence, we are using the docker container provided by the authors of the tool:
+
+- [google/deepvariant](https://hub.docker.com/r/google/deepvariant)
+
+This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/deepvariant) for convenience.
diff --git a/modules/nf-core/deepvariant/environment.yml b/modules/nf-core/deepvariant/environment.yml
diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf
@@ -2,6 +2,7 @@ process DEEPVARIANT {
     tag "$meta.id"
     label 'process_high'
 
+    //Conda is not supported at the moment
     container "nf-core/deepvariant:1.5.0"
 
     input:

diff --git a/modules/nf-core/gatk4/cnnscorevariants/README.md b/modules/nf-core/gatk4/cnnscorevariants/README.md
@@ -0,0 +1,9 @@
+# Conda is not supported at the moment
+
+The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811)
+
+Hence, we are using the docker container provided by the authors of the tool:
+
+- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk)
+
+This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience.
diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md b/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md
@@ -0,0 +1,9 @@
+# Conda is not supported at the moment
+
+The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811)
+
+Hence, we are using the docker container provided by the authors of the tool:
+
+- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk)
+
+This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience.
diff --git a/modules/nf-core/gatk4/germlinecnvcaller/README.md b/modules/nf-core/gatk4/germlinecnvcaller/README.md
@@ -0,0 +1,9 @@
+# Conda is not supported at the moment
+
+The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811)
+
+Hence, we are using the docker container provided by the authors of the tool:
+
+- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk)
+
+This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience.
diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md
@@ -0,0 +1,9 @@
+# Conda is not supported at the moment
+
+The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811)
+
+Hence, we are using the docker container provided by the authors of the tool:
+
+- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk)
+
+This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience.