nf-core · edmundmiller · Nov 28, 2024 · Nov 25, 2024 · Nov 25, 2024 · Nov 25, 2024
@@ -1,21 +1,33 @@
-FROM continuumio/miniconda3:4.9.2
-LABEL authors="Gisela Gabernet <[email protected]>,Edmund Miller <[email protected]>" \
-    description="Docker image containing Space Ranger"
+# syntax=docker/dockerfile:1
+
+FROM mambaorg/micromamba:1.5.10-noble
+ARG SPACERANGER_VER="3.1.2"
+# NOTE you need to go fill out the form to get a new download link
+ARG SPACERANGER_URL="https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-3.1.2.tar.gz?Expires=1732608367&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=S4jcGCs5H0wLFfREhSc~AfuPIOXE~PW96kX9o2EyxZnmn1goUecgfEWTj67fL1DnZJBIa06kFdUdNpsMn2ustiSWOfXEgjlYQnxIcNnQIiEBGoQTHWphvx3LEQ6wtZnkWS80P6IcE0HJkIsgy04t6Sohih5cxY4jgytYsrAfZDYr5G3KKFwTfCKmhzMaXqW635yPbyQ8xEcQHK0QwviAx8-EFq-PE8UzC4QgUKi2MW-ivcfZkSDSfF8C3s7SgwDXIGIWv52mzeszenxMjN4KrWQotZ7ZpktzI0Vfpz0dNC17dQeDQUHj4LuNYbdh3RqsPKtqu3wjCe2Q7KiyoWnmaw__" \"
+ARG SPACERANGER_SHA256="2566b24f29829b39f3add112a674990b1c54ae2fbe7ccb50a4c7dce9ccf152e6"
+LABEL org.opencontainers.image.authors="Gisela Gabernet <[email protected]>,Edmund Miller <[email protected]>"
+LABEL org.opencontainers.image.description="Docker image containing spaceranger"
+LABEL org.opencontainers.image.version="$SPACERANGER_VER"
+LABEL org.opencontainers.image.documentation="https://github.com/nf-core/modules/blob/master/modules/nf-core/spaceranger/README.md"
+LABEL org.opencontainers.image.source="https://github.com/nf-core/modules"
+LABEL org.opencontainers.image.vendor="nf-core"
+LABEL org.opencontainers.image.license="https://www.10xgenomics.com/support/software/space-ranger/downloads/eula"
 # Disclaimer: this container is not provided nor supported by 10x Genomics.
 
 # Install procps and curl and clean apt cache
-RUN apt-get update --allow-releaseinfo-change \
-    && apt-get install -y procps curl \
-    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+RUN micromamba install -y -n base conda-forge::procps-ng \
+    && micromamba clean -a -y
+USER root
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
 
-# Copy pre-downloaded spaceranger file
-ENV SPACERANGER_VER 3.0.0
-COPY spaceranger-$SPACERANGER_VER.tar.gz /opt/spaceranger-$SPACERANGER_VER.tar.gz
+# NOTE Docker doesn't support md5sum and that's what spaceranger gives us --checksum=md5sum:949088b1e2cc5bd03079b60a65b41d39
+# https://docs.docker.com/reference/dockerfile/#add---checksum
+ADD --checksum=sha256:$SPACERANGER_SHA256 \
+    $SPACERANGER_URL \
+    /opt/spaceranger-$SPACERANGER_VER.tar.gz
 
 # Install spaceranger
-RUN \
-    cd /opt && \
-    tar -xzvf spaceranger-$SPACERANGER_VER.tar.gz && \
-    export PATH=/opt/spaceranger-$SPACERANGER_VER:$PATH && \
-    ln -s /opt/spaceranger-$SPACERANGER_VER/spaceranger /usr/bin/spaceranger && \
-    rm -rf /opt/spaceranger-$SPACERANGER_VER.tar
+RUN tar -xzf /opt/spaceranger-$SPACERANGER_VER.tar.gz -C /opt/ \
+    && rm /opt/spaceranger-$SPACERANGER_VER.tar.gz \
+    && ln -s /opt/spaceranger-$SPACERANGER_VER/spaceranger /usr/bin/spaceranger
+ENV PATH="/opt/spaceranger-$SPACERANGER_VER:$PATH"
diff --git a/modules/nf-core/spaceranger/README.md b/modules/nf-core/spaceranger/README.md
@@ -2,17 +2,17 @@
 
 Space Ranger is a commercial tool by 10X Genomics. The container provided for the spaceranger nf-core module is not provided nor supported by 10x Genomics. Updating the Space Ranger version in the container and pushing the update to Dockerhub needs to be done manually.
 
-1. Navigate to the [Space Ranger download page](https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest) and download the tar ball of the desired Space Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
+1. Navigate to the [Space Ranger download page](https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest) and get a link for the Space Ranger downloads
 
-2. Edit the Dockerfile: update the Cell Ranger version in this line:
+2. Edit the Dockerfile: update the Space Ranger version in this line:
 
-   ```bash
-   ENV SPACERANGER_VER <VERSION>
-   ```
+```diff
+- ARG SPACERANGER_VER="3.1.2"
++ ARG SPACERANGER_VER="4.0.0"
+- ARG SPACERANGER_URL="https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-3.1.2.tar.gz?Expires=1732608367&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=S4jcGCs5H0wLFfREhSc~AfuPIOXE~PW96kX9o2EyxZnmn1goUecgfEWTj67fL1DnZJBIa06kFdUdNpsMn2ustiSWOfXEgjlYQnxIcNnQIiEBGoQTHWphvx3LEQ6wtZnkWS80P6IcE0HJkIsgy04t6Sohih5cxY4jgytYsrAfZDYr5G3KKFwTfCKmhzMaXqW635yPbyQ8xEcQHK0QwviAx8-EFq-PE8UzC4QgUKi2MW-ivcfZkSDSfF8C3s7SgwDXIGIWv52mzeszenxMjN4KrWQotZ7ZpktzI0Vfpz0dNC17dQeDQUHj4LuNYbdh3RqsPKtqu3wjCe2Q7KiyoWnmaw__" \"
++ ARG SPACERANGER_URL="<Your-unique-download-link-that-expires"
+- ARG SPACERANGER_SHA256="2566b24f29829b39f3add112a674990b1c54ae2fbe7ccb50a4c7dce9ccf152e6"
++ ARG SPACERANGER_SHA256="<Manual SHA256 of tar.gz>"
+```
 
-3. Create the container:
-
-   ```bash
-   docker build . -t quay.io/nf-core/spaceranger:<VERSION>
-   docker push quay.io/nf-core/spaceranger:<VERSION>
-   ```
+3. Push the changes and the Dockerfile should be built and uploaded to `quay.io/nf-core/modules/spaceranger`!
diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf
@@ -2,7 +2,7 @@ process SPACERANGER_COUNT {
     tag "$meta.id"
     label 'process_high'
 
-    container "nf-core/spaceranger:3.0.0"
+    container "nf-core/modules/spaceranger:d71611e316a8614b"
 
     input:
     tuple val(meta), path(reads), path(image), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile)

diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test b/modules/nf-core/spaceranger/count/tests/main.nf.test
@@ -68,7 +68,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
+                    path(process.out.versions.get(0)).yaml,
                     process.out.outs.get(0).get(1).findAll { file(it).name !in [
                         'web_summary.html',
                         'scalefactors_json.json',
@@ -144,7 +144,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match() },
             )
         }
     }
@@ -204,7 +204,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
+                    path(process.out.versions.get(0)).yaml,
                     process.out.outs.get(0).get(1).findAll { file(it).name !in [
                         'web_summary.html',
                         'scalefactors_json.json',

diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test.snap b/modules/nf-core/spaceranger/count/tests/main.nf.test.snap
@@ -1,90 +1,96 @@
 {
     "spaceranger v1 (stub) - homo_sapiens - fasta - gtf - fastq - tif - csv": {
         "content": [
-            [
-                "versions.yml:md5,1539e8a9a3d63ce3653920721d1af509"
-            ]
+            {
+                "SPACERANGER_COUNT": {
+                    "spaceranger": "3.1.2"
+                }
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-04-02T09:29:02.205153668"
+        "timestamp": "2024-11-26T01:48:31.348979531"
     },
     "spaceranger v2 - homo_sapiens - fasta - gtf - fastq - tif - csv": {
         "content": [
+            {
+                "SPACERANGER_COUNT": {
+                    "spaceranger": "3.1.2"
+                }
+            },
             [
-                "versions.yml:md5,1539e8a9a3d63ce3653920721d1af509"
-            ],
-            [
-                "clusters.csv:md5,2cc2d0c94ec0af69f03db235f9ea6932",
-                "clusters.csv:md5,46c12f3845e28f27f2cd580cb004c0ea",
-                "clusters.csv:md5,4e5f082240b9c9903168842d1f9dbe34",
-                "clusters.csv:md5,e626eb7049baf591ea49f5d8c305621c",
-                "clusters.csv:md5,65cfb24fc937e4df903a742c1adf8b08",
-                "clusters.csv:md5,819a71787618945dacfa2d5301b953b1",
-                "clusters.csv:md5,5ae17ed02cdb9f61d7ceb0cd6922c9d4",
-                "clusters.csv:md5,641550bec22e02fff3611087f7fd6e07",
-                "clusters.csv:md5,9fbe5c79035175bc1899e9a7fc80f7ac",
-                "clusters.csv:md5,ed0c2dcca15c14a9983407ff9af0daaf",
-                "differential_expression.csv:md5,d37a8ef21699372ec4a4bdf0c43d71b7",
-                "differential_expression.csv:md5,ac3181524385c88d38a0fc17d3bdd526",
-                "differential_expression.csv:md5,557d6dfec7421c392aa6443725608cd1",
-                "differential_expression.csv:md5,1437fad68d701c97a4a46318aee45575",
-                "differential_expression.csv:md5,7a2f3d0e90782055580f4903617a7d27",
-                "differential_expression.csv:md5,41756e9570d07aee6aed710e6a965846",
-                "differential_expression.csv:md5,62ea7651c3f195d3c960c6c688dca477",
-                "differential_expression.csv:md5,b630542266c4abb71f4205922340498d",
-                "differential_expression.csv:md5,0deb97f0be7e72ad73e456092db31e6d",
-                "differential_expression.csv:md5,3bba8490f753507e7e2e29be759f218b",
-                "components.csv:md5,568bb9bcb6ee913356fcb4be3fea1911",
-                "dispersion.csv:md5,e2037b1db404f6e5d8b3144629f2500d",
-                "features_selected.csv:md5,3ba6d1315ae594963b306d94ba1180e7",
-                "projection.csv:md5,aef5d71381678d5245e471f3d5a8ab67",
-                "variance.csv:md5,475a95e51ce66e639ae21d801c455e2b",
-                "projection.csv:md5,928c0f68a9c773fba590941d3d5af7ca",
-                "projection.csv:md5,216dcc5589a083fcc27d981aa90fa2ab",
-                "filtered_feature_bc_matrix.h5:md5,f1a8f225c113974b47efffe08e70f367",
-                "metrics_summary.csv:md5,faa17487b479eab361050d3266da2efb",
+                "clusters.csv:md5,221a4554e62ea94b0df8dbf637d2c13c",
+                "clusters.csv:md5,53ee76645943b5562392aac51d2d9f3f",
+                "clusters.csv:md5,b791359469683ad19cdb8d1af3de5705",
+                "clusters.csv:md5,9a4f9148e0e834c1127bf8393ece6330",
+                "clusters.csv:md5,c11bcc64f870469ab2f136d9272a7a6d",
+                "clusters.csv:md5,488846bbb469365e199928c7a440320a",
+                "clusters.csv:md5,5941f7e847d35a4f06d3631e21d2eb9d",
+                "clusters.csv:md5,d244d405c32766339d2b7a3fa8bf8cee",
+                "clusters.csv:md5,981386408cd953548994c31253e787de",
+                "clusters.csv:md5,24c4f13449e5362fcbcd41b9ff413992",
+                "differential_expression.csv:md5,589c1bd4529f092bb1d332e7da561dad",
+                "differential_expression.csv:md5,d9d978b398b33ac9687b44531909e0cd",
+                "differential_expression.csv:md5,4edbc893280f9d03c3de00a503e86f8c",
+                "differential_expression.csv:md5,316181d501c495384016227309856b09",
+                "differential_expression.csv:md5,dae49941396609fb08df13b82fe89151",
+                "differential_expression.csv:md5,4a13ae44c8454dbcb0298eb63df8b8e8",
+                "differential_expression.csv:md5,eeb02c4afe1f49d5502fb024b25b2c38",
+                "differential_expression.csv:md5,9a456828fe5d762e6e07383da5c2791d",
+                "differential_expression.csv:md5,bcbd1504976824e9f4d20a8dd36e2a1f",
+                "differential_expression.csv:md5,3ad93fc4d52950cfede885dc58cd2823",
+                "components.csv:md5,811a32dce6c795e958dc4bc635ee53be",
+                "dispersion.csv:md5,64c2e57ef0ca9a80cce8b952c81b62f5",
+                "features_selected.csv:md5,bd0c0a20b0b0009df796e8a755d028c1",
+                "projection.csv:md5,e530c925a185965514fa82f4da83fa81",
+                "variance.csv:md5,4159711ab5d64e97737fad9d75d945b3",
+                "projection.csv:md5,ce729f7e237df4570ac3e4a79251df24",
+                "projection.csv:md5,fa7bdefa8424b233fe6461129ab76d57",
+                "filtered_feature_bc_matrix.h5:md5,f625d7e2c063c8c079ccc35a853b356d",
+                "metrics_summary.csv:md5,5ece84f5f8e08839749b1c8f2bff6701",
                 "probe_set.csv:md5,5bfb8f12319be1b2b6c14142537c3804",
-                "raw_feature_bc_matrix.h5:md5,6e40ae93a116c6fc0adbe707b0eb415f",
-                "raw_probe_bc_matrix.h5:md5,3d5e711d0891ca2caaf301a2c1fbda91",
+                "raw_feature_bc_matrix.h5:md5,90575715eb252f0b652c9d36a1f5628e",
+                "raw_probe_bc_matrix.h5:md5,8ab08437814506f98e3f10107cfc38ac",
                 "aligned_fiducials.jpg:md5,51dcc3a32d3d5ca4704f664c8ede81ef",
                 "cytassist_image.tiff:md5,0fb04a55e5658f4d158d986a334b034d",
-                "detected_tissue_image.jpg:md5,1d3ccc1e12c4fee091b006e48b9cc16a",
-                "spatial_enrichment.csv:md5,1117792553e82feb2b4b3934907a0136",
+                "detected_tissue_image.jpg:md5,11c9fa90913b5c6e93cecdb8f53d58db",
+                "spatial_enrichment.csv:md5,4379bc4fef891b45ff9264ee8c408bd0",
                 "tissue_hires_image.png:md5,834706fff299024fab48e6366afc9cb9",
                 "tissue_lowres_image.png:md5,8c1fcb378f7f886301f49ffc4f84360a",
-                "tissue_positions.csv:md5,425601ef21661ec0126000f905ef044f"
+                "tissue_positions.csv:md5,930aeb2b790032337d91dd27cc70f135"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-04-02T10:13:00.787792273"
+        "timestamp": "2024-11-26T01:58:16.555517048"
     },
     "spaceranger v1 - homo_sapiens - fasta - gtf - fastq - tif - csv": {
         "content": [
+            {
+                "SPACERANGER_COUNT": {
+                    "spaceranger": "3.1.2"
+                }
+            },
             [
-                "versions.yml:md5,1539e8a9a3d63ce3653920721d1af509"
-            ],
-            [
-                "filtered_feature_bc_matrix.h5:md5,7e09d1cd2e1f497a698c5efde9e4af84",
-                "metrics_summary.csv:md5,07a6fcc2e20f854f8d3fcde2457a2f9a",
-                "molecule_info.h5:md5,1f2e0fd31d15509e7916e84f22632c9c",
-                "raw_feature_bc_matrix.h5:md5,5a4184a3bfaf722eec8d1a763a45906e",
+                "filtered_feature_bc_matrix.h5:md5,a756f6dda550f52f9fb3e347207a2c6c",
+                "metrics_summary.csv:md5,38774fc5f54873d711b4898a2dd50e72",
+                "molecule_info.h5:md5,9e6393dbbccdfe58edf9e92181261f88",
+                "raw_feature_bc_matrix.h5:md5,860702876f936f89fdcec2b5f599a7d2",
                 "aligned_fiducials.jpg:md5,f6217ddd707bb189e665f56b130c3da8",
                 "detected_tissue_image.jpg:md5,c1c7e8741701a576c1ec103c1aaf98ea",
                 "tissue_hires_image.png:md5,d91f8f176ae35ab824ede87117ac0889",
                 "tissue_lowres_image.png:md5,475a04208d193191c84d7a3b5d4eb287",
-                "tissue_positions.csv:md5,748bf590c445db409d7dbdf5a08e72e8"
+                "tissue_positions.csv:md5,7f9cb407b3dd69726a12967b979a5624"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-04-02T09:37:13.128424153"
+        "timestamp": "2024-11-26T01:48:13.569651476"
     }
 }
diff --git a/modules/nf-core/spaceranger/mkgtf/main.nf b/modules/nf-core/spaceranger/mkgtf/main.nf
@@ -2,7 +2,7 @@ process SPACERANGER_MKGTF {
     tag "$gtf"
     label 'process_low'
 
-    container "nf-core/spaceranger:3.0.0"
+    container "nf-core/modules/spaceranger:d71611e316a8614b"
 
     input:
     path gtf

diff --git a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test
@@ -24,7 +24,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.gtf,
+                    path(process.out.versions.get(0)).yaml,
+                ).match() }
             )
         }
 

diff --git a/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test.snap b/modules/nf-core/spaceranger/mkgtf/tests/main.nf.test.snap
@@ -1,25 +1,19 @@
 {
     "homo_sapiens - gtf": {
         "content": [
+            [
+                "genome.filtered.gtf:md5,50fc877b1c53b36b3b413aff88bda48c"
+            ],
             {
-                "0": [
-                    "genome.filtered.gtf:md5,50fc877b1c53b36b3b413aff88bda48c"
-                ],
-                "1": [
-                    "versions.yml:md5,2e30a28641165e16d77eec844cbaffe5"
-                ],
-                "gtf": [
-                    "genome.filtered.gtf:md5,50fc877b1c53b36b3b413aff88bda48c"
-                ],
-                "versions": [
-                    "versions.yml:md5,2e30a28641165e16d77eec844cbaffe5"
-                ]
+                "SPACERANGER_MKGTF": {
+                    "spaceranger": "3.1.2"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-04-02T09:29:35.376030595"
+        "timestamp": "2024-11-26T01:58:29.469616437"
     }
 }
diff --git a/modules/nf-core/spaceranger/mkref/main.nf b/modules/nf-core/spaceranger/mkref/main.nf
@@ -2,7 +2,7 @@ process SPACERANGER_MKREF {
     tag "$fasta"
     label 'process_high'
 
-    container "nf-core/spaceranger:3.0.0"
+    container "nf-core/modules/spaceranger:d71611e316a8614b"
 
     input:
     path fasta
@@ -41,4 +41,37 @@ process SPACERANGER_MKREF {
         spaceranger: \$(spaceranger -V | sed -e "s/spaceranger spaceranger-//g")
     END_VERSIONS
     """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "SPACERANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    """
+    mkdir -p $reference_name
+
+    touch ${reference_name}/genome.fa
+    touch ${reference_name}/genome.fa.fai
+    touch ${reference_name}/genes.gtf.gz
+    touch ${reference_name}/reference.json
+    touch ${reference_name}/Genome
+    touch ${reference_name}/SA
+    touch ${reference_name}/SAindex
+    touch ${reference_name}/chrLength.txt
+    touch ${reference_name}/chrName.txt
+    touch ${reference_name}/chrNameLength.txt
+    touch ${reference_name}/chrStart.txt
+    touch ${reference_name}/exonGeTrInfo.tab
+    touch ${reference_name}/exonInfo.tab
+    touch ${reference_name}/geneInfo.tab
+    touch ${reference_name}/sjdbInfo.txt
+    touch ${reference_name}/sjdbList.fromGTF.out.tab
+    touch ${reference_name}/sjdbList.out.tab
+    touch ${reference_name}/transcriptInfo.tab
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        spaceranger: \$(spaceranger -V | sed -e "s/spaceranger spaceranger-//g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/spaceranger/mkref/tests/main.nf.test b/modules/nf-core/spaceranger/mkref/tests/main.nf.test
@@ -25,7 +25,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
+                    path(process.out.versions.get(0)).yaml,
                     "${process.out.reference[0]}/fasta",
                     "${process.out.reference[0]}/genes",
                     "${process.out.reference[0]}/reference.json",