Merge pull request #1286 from AlexsLemonade/jashapiro/v0.10.2

Bugfix + changelog  + 0.10.2 updates

Author: jashapiro

CHANGELOG.md

@@ -86,7 +86,9 @@ def rewrite_markers(
     out_cols = ["id", "symbol", "z_score|float"] + other_cols
 
     for cluster_name, group in markers.groupby(cluster_col, sort=False):
-        out_path = markers_out_dir / (make_cluster_filename(cluster_name) + ".tsv.gz")
+        out_path = markers_out_dir / (
+            make_cluster_filename(str(cluster_name)) + ".tsv.gz"
+        )
         group[out_cols].to_csv(out_path, sep="\t", index=False, compression="gzip")
 
     return True

bin/cellbrowser_rewritemarkers.py

@@ -1,4 +1,4 @@
-# scpca-nf v0.10.1
+# scpca-nf v0.10.2
 
 
 The  `scpca-nf` workflow is used to process 10x single-cell data as part of the [Single-cell Pediatric Cancer Atlas (ScPCA) project](https://scpca.alexslemonade.org/).

cavatica/sb_doc.md

@@ -3,7 +3,7 @@ app_content:
   executor_version: 24.10.6
 class: nextflow
 cwlVersion: None
-doc: "# scpca-nf v0.10.1
+doc: "# scpca-nf v0.10.2
 
 
   The `scpca-nf` workflow is used to process 10x single-cell data as part of the

cavatica/sb_nextflow_schema.yaml

@@ -15,6 +15,7 @@ Cavatica
 cDNA
 CellAssign
 cellhash
+changelog
 CLI
 CNV
 conda
@@ -29,26 +30,30 @@ Dockerfile
 doi
 DS
 DV
+EBS
 ECR
 EFO
 embeddings
 Ensembl
 et
 falsey
-FASTQ
 fastq
+FASTQ
 FFPE
 formatter
 GEX
+GHA
 Github
 glioblastoma
 GRCh
 HD
+HDF
 Heimberg
 Hippen
 HPC
 HTO
 HTOs
+HVG
 HVGs
 Ichihara
 inferCNV
@@ -65,6 +70,7 @@ Nextflow
 Nextflow's
 nf
 oligos
+OpenScPCA
 PanglaoDB
 parallelizing
 PBMCs
@@ -76,8 +82,8 @@ README
 reproducibility
 reproducibly
 SCE
-ScPCA
 scpca
+ScPCA
 Seqera
 singleplexed
 SingleR

components/dictionary.txt

@@ -96,12 +96,12 @@ Using the above command will run the workflow from the `main` branch of the work
 To update to the latest released version you can run `nextflow pull AlexsLemonade/scpca-nf` before the `nextflow run` command.
 
 To be sure that you are using a consistent version, you can specify use of a release tagged version of the workflow, set below with the `-r` flag.
-The command below will pull the `scpca-nf` workflow directly from Github using the `v0.10.1` version.
+The command below will pull the `scpca-nf` workflow directly from Github using the `v0.10.2` version.
 Released versions can be found on the [`scpca-nf` repository releases page](https://github.com/AlexsLemonade/scpca-nf/releases).
 
 ```sh
 nextflow run AlexsLemonade/scpca-nf \
-  -r v0.10.1 \
+  -r v0.10.2 \
   -config {path to config file}  \
   -profile {name of profile}
 ```
@@ -332,7 +332,7 @@ If you will be analyzing spatial expression data, you will also need the Cell Ra
 
 If your compute nodes do not have internet access, you will likely have to pre-pull the required container images as well.
 When doing this, it is important to be sure that you also specify the revision (version tag) of the `scpca-nf` workflow that you are using.
-For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.10.1`, then you will want to set `-r v0.10.1` for `get_refs.py` as well to be sure you have the correct containers.
+For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.10.2`, then you will want to set `-r v0.10.2` for `get_refs.py` as well to be sure you have the correct containers.
 By default, `get_refs.py` will download files and images associated with the latest release.
 
 If your system uses Docker, you can add the `--docker` flag:

external-instructions.md

@@ -6,7 +6,7 @@ manifest {
   mainScript = 'main.nf'
   defaultBranch = 'main'
   nextflowVersion = '>=24.09'
-  version = 'v0.10.1'
+  version = 'v0.10.2'
   contributors = [
     [
       name: "Allegra Hawkins",

nextflow.config

@@ -640,12 +640,12 @@
         },
         "cellbrowser_container": {
           "type": "string",
-          "default": "ghcr.io/alexslemonade/scpca-nf/cellbrowser:v0.10.1",
+          "default": "ghcr.io/alexslemonade/scpca-nf/cellbrowser:v0.10.2",
           "fa_icon": "fab fa-docker"
         },
         "vireo_container": {
           "type": "string",
-          "default": "ghcr.io/alexslemonade/scpca-nf/vireo-snp:v0.10.1",
+          "default": "ghcr.io/alexslemonade/scpca-nf/vireo-snp:v0.10.2",
           "hidden": true,
           "fa_icon": "fab fa-docker"
         },