Deploy for release 0.1.1 from f639468

czbiohub-sf · May 3, 2023 · e62fdec · e62fdec
1 parent 6c80d2f
commit e62fdec
Show file tree

Hide file tree

Showing 36 changed files with 51 additions and 52 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,8 @@
 # utilities 0.1.1
 
-* `mapping/process_10x_auto`: Allow grouping input fastqs per folder or via a custom regex statement.
+* `mapping/process_smartseq2_auto`: Allow grouping input fastqs per folder or via a custom regex statement.
 
-* `mapping/process_10x_auto`: Add more documentation to the arguments to clarify regex usage.
+* `mapping/process_smartseq2_auto`: Add more documentation to the arguments to clarify regex usage.
 
 # utilities 0.1.0
 

diff --git a/src/mapping/process_smartseq2/auto.vsh.yaml b/src/mapping/process_smartseq2/auto.vsh.yaml
@@ -11,11 +11,10 @@ functionality:
       * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.
       * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.
       * Write the list of samples as a yaml in the output directory.
-      * Map the reads using Cell Ranger
-      * Convert the Cell Ranger output to h5mu
-      * Remove ambient RNA with CellBender
-      * Remove cells with less than 100 genes or 1000 reads.
-      * Make the cell names unique
+      * Map the reads using Star
+      * Sort counts with samtools
+      * Convert to count table with HTSeq
+      * Compute QC metrics with MultiQC
       * Output one h5mu file per sample
 
     Concatenating the invididual h5mu files into one h5mu file is a separate pipeline.

diff --git a/target/docker/demux/spaceranger_mkfastq/.config.vsh.yaml b/target/docker/demux/spaceranger_mkfastq/.config.vsh.yaml
@@ -79,5 +79,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/docker/demux/spaceranger_mkfastq"
   executable: "/home/runner/work/utilities/utilities/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq b/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq
@@ -399,9 +399,9 @@ FROM ghcr.io/data-intuitive/spaceranger:latest
 
 RUN :
 LABEL org.opencontainers.image.description="Companion container for running component demux spaceranger_mkfastq"
-LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z"
+LABEL org.opencontainers.image.created="2023-05-03T21:05:52Z"
 LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
-LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20"
 LABEL org.opencontainers.image.version="0.1.1"
 VIASHDOCKER
 }

diff --git a/target/docker/mapping/spaceranger_count/.config.vsh.yaml b/target/docker/mapping/spaceranger_count/.config.vsh.yaml
@@ -129,5 +129,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/docker/mapping/spaceranger_count"
   executable: "/home/runner/work/utilities/utilities/target/docker/mapping/spaceranger_count/spaceranger_count"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/docker/mapping/spaceranger_count/spaceranger_count b/target/docker/mapping/spaceranger_count/spaceranger_count
@@ -423,9 +423,9 @@ FROM ghcr.io/data-intuitive/spaceranger:latest
 
 RUN :
 LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
-LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z"
+LABEL org.opencontainers.image.created="2023-05-03T21:05:53Z"
 LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
-LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20"
 LABEL org.opencontainers.image.version="0.1.1"
 VIASHDOCKER
 }

diff --git a/target/docker/multiomics/cellranger_arc_aggr/.config.vsh.yaml b/target/docker/multiomics/cellranger_arc_aggr/.config.vsh.yaml
@@ -105,5 +105,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_aggr"
   executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr b/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr
@@ -418,9 +418,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "numpy" "pandas" "scanpy"
 
 LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_arc_aggr"
-LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z"
+LABEL org.opencontainers.image.created="2023-05-03T21:05:53Z"
 LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
-LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20"
 LABEL org.opencontainers.image.version="0.1.1"
 VIASHDOCKER
 }

diff --git a/target/docker/multiomics/cellranger_arc_count/.config.vsh.yaml b/target/docker/multiomics/cellranger_arc_count/.config.vsh.yaml
@@ -97,5 +97,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_count"
   executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count b/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count
@@ -416,9 +416,9 @@ FROM ghcr.io/data-intuitive/cellranger_arc:2.0
 
 RUN :
 LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_arc_count"
-LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z"
+LABEL org.opencontainers.image.created="2023-05-03T21:05:53Z"
 LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
-LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20"
 LABEL org.opencontainers.image.version="0.1.1"
 VIASHDOCKER
 }

diff --git a/target/docker/multiomics/cellranger_cite_seq/.config.vsh.yaml b/target/docker/multiomics/cellranger_cite_seq/.config.vsh.yaml
@@ -95,5 +95,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_cite_seq"
   executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq b/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq
@@ -409,9 +409,9 @@ FROM ghcr.io/data-intuitive/cellranger_arc:2.0
 
 RUN :
 LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_cite_seq"
-LABEL org.opencontainers.image.created="2023-05-03T20:09:53Z"
+LABEL org.opencontainers.image.created="2023-05-03T21:05:54Z"
 LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
-LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20"
 LABEL org.opencontainers.image.version="0.1.1"
 VIASHDOCKER
 }

diff --git a/target/docker/operations/create_runner_script/.config.vsh.yaml b/target/docker/operations/create_runner_script/.config.vsh.yaml
@@ -122,5 +122,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/docker/operations/create_runner_script"
   executable: "/home/runner/work/utilities/utilities/target/docker/operations/create_runner_script/create_runner_script"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/docker/operations/create_runner_script/create_runner_script b/target/docker/operations/create_runner_script/create_runner_script
@@ -426,9 +426,9 @@ FROM python:3.10
 
 RUN :
 LABEL org.opencontainers.image.description="Companion container for running component operations create_runner_script"
-LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z"
+LABEL org.opencontainers.image.created="2023-05-03T21:05:52Z"
 LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
-LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20"
 LABEL org.opencontainers.image.version="0.1.1"
 VIASHDOCKER
 }

diff --git a/target/native/demux/spaceranger_mkfastq/.config.vsh.yaml b/target/native/demux/spaceranger_mkfastq/.config.vsh.yaml
@@ -79,5 +79,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/native/demux/spaceranger_mkfastq"
   executable: "/home/runner/work/utilities/utilities/target/native/demux/spaceranger_mkfastq/spaceranger_mkfastq"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/native/mapping/spaceranger_count/.config.vsh.yaml b/target/native/mapping/spaceranger_count/.config.vsh.yaml
@@ -129,5 +129,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/native/mapping/spaceranger_count"
   executable: "/home/runner/work/utilities/utilities/target/native/mapping/spaceranger_count/spaceranger_count"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/native/multiomics/cellranger_arc_aggr/.config.vsh.yaml b/target/native/multiomics/cellranger_arc_aggr/.config.vsh.yaml
@@ -105,5 +105,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_aggr"
   executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_aggr/cellranger_arc_aggr"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/native/multiomics/cellranger_arc_count/.config.vsh.yaml b/target/native/multiomics/cellranger_arc_count/.config.vsh.yaml
@@ -97,5 +97,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_count"
   executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_count/cellranger_arc_count"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/native/multiomics/cellranger_cite_seq/.config.vsh.yaml b/target/native/multiomics/cellranger_cite_seq/.config.vsh.yaml
@@ -95,5 +95,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_cite_seq"
   executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_cite_seq/cellranger_cite_seq"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/native/operations/create_runner_script/.config.vsh.yaml b/target/native/operations/create_runner_script/.config.vsh.yaml
@@ -122,5 +122,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/native/operations/create_runner_script"
   executable: "/home/runner/work/utilities/utilities/target/native/operations/create_runner_script/create_runner_script"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/nextflow/demux/spaceranger_mkfastq/.config.vsh.yaml b/target/nextflow/demux/spaceranger_mkfastq/.config.vsh.yaml
@@ -79,5 +79,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/nextflow/demux/spaceranger_mkfastq"
   executable: "/home/runner/work/utilities/utilities/target/nextflow/demux/spaceranger_mkfastq/spaceranger_mkfastq"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/nextflow/demux/spaceranger_mkfastq/main.nf b/target/nextflow/demux/spaceranger_mkfastq/main.nf
@@ -123,7 +123,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
     "config" : "/home/runner/work/utilities/utilities/src/demux/spaceranger_mkfastq/config.vsh.yaml",
     "platform" : "nextflow",
     "viash_version" : "0.7.3",
-    "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b",
+    "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20",
     "git_remote" : "https://github.com/czbiohub/utilities"
   }
 }'''))

diff --git a/target/nextflow/mapping/process_10x/.config.vsh.yaml b/target/nextflow/mapping/process_10x/.config.vsh.yaml
@@ -105,5 +105,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x"
   executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x/process_10x"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/nextflow/mapping/process_10x/main.nf b/target/nextflow/mapping/process_10x/main.nf
@@ -168,7 +168,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
     "config" : "/home/runner/work/utilities/utilities/src/mapping/process_10x/config.vsh.yaml",
     "platform" : "nextflow",
     "viash_version" : "0.7.3",
-    "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b",
+    "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20",
     "git_remote" : "https://github.com/czbiohub/utilities"
   }
 }'''))

diff --git a/target/nextflow/mapping/process_10x_auto/.config.vsh.yaml b/target/nextflow/mapping/process_10x_auto/.config.vsh.yaml
@@ -150,5 +150,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x_auto"
   executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x_auto/process_10x_auto"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/nextflow/mapping/process_10x_auto/main.nf b/target/nextflow/mapping/process_10x_auto/main.nf
@@ -208,7 +208,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
     "config" : "/home/runner/work/utilities/utilities/src/mapping/process_10x/auto.vsh.yaml",
     "platform" : "nextflow",
     "viash_version" : "0.7.3",
-    "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b",
+    "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20",
     "git_remote" : "https://github.com/czbiohub/utilities"
   }
 }'''))

diff --git a/target/nextflow/mapping/process_smartseq2/.config.vsh.yaml b/target/nextflow/mapping/process_smartseq2/.config.vsh.yaml
@@ -146,5 +146,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2"
   executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2/process_smartseq2"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/nextflow/mapping/process_smartseq2/main.nf b/target/nextflow/mapping/process_smartseq2/main.nf
@@ -216,7 +216,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
     "config" : "/home/runner/work/utilities/utilities/src/mapping/process_smartseq2/config.vsh.yaml",
     "platform" : "nextflow",
     "viash_version" : "0.7.3",
-    "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b",
+    "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20",
     "git_remote" : "https://github.com/czbiohub/utilities"
   }
 }'''))

diff --git a/target/nextflow/mapping/process_smartseq2_auto/.config.vsh.yaml b/target/nextflow/mapping/process_smartseq2_auto/.config.vsh.yaml
@@ -153,10 +153,10 @@ functionality:
     \ name using the same `fastq_regex` and `sample_id_replacement`.\n  * Detect cell\
     \ ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n\
     \  * Write the list of samples as a yaml in the output directory.\n  * Map the\
-    \ reads using Cell Ranger\n  * Convert the Cell Ranger output to h5mu\n  * Remove\
-    \ ambient RNA with CellBender\n  * Remove cells with less than 100 genes or 1000\
-    \ reads.\n  * Make the cell names unique\n  * Output one h5mu file per sample\n\
-    \nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n"
+    \ reads using Star\n  * Sort counts with samtools\n  * Convert to count table\
+    \ with HTSeq\n  * Compute QC metrics with MultiQC\n  * Output one h5mu file per\
+    \ sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate\
+    \ pipeline.\n"
   status: "enabled"
   set_wd_to_resources_dir: false
 platforms:
@@ -178,5 +178,5 @@ info:
   output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2_auto"
   executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2_auto/process_smartseq2_auto"
   viash_version: "0.7.3"
-  git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b"
+  git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20"
   git_remote: "https://github.com/czbiohub/utilities"
diff --git a/target/nextflow/mapping/process_smartseq2_auto/main.nf b/target/nextflow/mapping/process_smartseq2_auto/main.nf
@@ -216,7 +216,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
         "entrypoint" : "auto"
       }
     ],
-    "description" : "Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n  * Look for all `*.fastq.gz` files in the `input_dir` which\n    match the regular expression in `fastq_regex`.\n  * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n  * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n  * Write the list of samples as a yaml in the output directory.\n  * Map the reads using Cell Ranger\n  * Convert the Cell Ranger output to h5mu\n  * Remove ambient RNA with CellBender\n  * Remove cells with less than 100 genes or 1000 reads.\n  * Make the cell names unique\n  * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n",
+    "description" : "Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n  * Look for all `*.fastq.gz` files in the `input_dir` which\n    match the regular expression in `fastq_regex`.\n  * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n  * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n  * Write the list of samples as a yaml in the output directory.\n  * Map the reads using Star\n  * Sort counts with samtools\n  * Convert to count table with HTSeq\n  * Compute QC metrics with MultiQC\n  * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n",
     "status" : "enabled",
     "set_wd_to_resources_dir" : false
   },
@@ -242,7 +242,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
     "config" : "/home/runner/work/utilities/utilities/src/mapping/process_smartseq2/auto.vsh.yaml",
     "platform" : "nextflow",
     "viash_version" : "0.7.3",
-    "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b",
+    "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20",
     "git_remote" : "https://github.com/czbiohub/utilities"
   }
 }'''))

diff --git a/target/nextflow/mapping/process_smartseq2_auto/nextflow.config b/target/nextflow/mapping/process_smartseq2_auto/nextflow.config
@@ -3,6 +3,6 @@ manifest {
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
   version = '0.1.1'
-  description = 'Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n  * Look for all `*.fastq.gz` files in the `input_dir` which\n    match the regular expression in `fastq_regex`.\n  * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n  * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n  * Write the list of samples as a yaml in the output directory.\n  * Map the reads using Cell Ranger\n  * Convert the Cell Ranger output to h5mu\n  * Remove ambient RNA with CellBender\n  * Remove cells with less than 100 genes or 1000 reads.\n  * Make the cell names unique\n  * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n'
+  description = 'Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n  * Look for all `*.fastq.gz` files in the `input_dir` which\n    match the regular expression in `fastq_regex`.\n  * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n  * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n  * Write the list of samples as a yaml in the output directory.\n  * Map the reads using Star\n  * Sort counts with samtools\n  * Convert to count table with HTSeq\n  * Compute QC metrics with MultiQC\n  * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n'
   author = 'Angela Pisco, Robrecht Cannoodt'
 }