Merge pull request #307 from AlexsLemonade/sjspielman/cut-feature-sal…

…mon-index Cut feature barcode file for salmon indexing
AlexsLemonade · May 5, 2023 · a6b87e4 · a6b87e4
2 parents 97c3035 + 8c3f516
commit a6b87e4
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Showing 4 changed files with 9 additions and 6 deletions.
diff --git a/external-instructions.md b/external-instructions.md
@@ -63,7 +63,7 @@ nextflow run AlexsLemonade/scpca-nf \
 ```
 
 Where `<path to config file>` is the **relative** path to the [configuration file](#configuration-files) that you have setup and `<name of profile>` is the name of the profile that you chose when [creating a profile](#setting-up-a-profile-in-the-configuration-file).
-This command will pull the `scpca-nf` workflow directly from Github, using the `v0.4.1` version, and run it based on the settings in the configuration file that you have defined.
+This command will pull the `scpca-nf` workflow directly from Github, using the `v0.4.2` version, and run it based on the settings in the configuration file that you have defined.
 
 **Note:** `scpca-nf` is under active development.
 Using the above command will run the workflow from the `main` branch of the workflow repository.
@@ -74,7 +74,7 @@ Released versions can be found on the [`scpca-nf` repo releases page](https://gi
 
 ```sh
 nextflow run AlexsLemonade/scpca-nf \
-  -r v0.4.1 \
+  -r v0.4.2 \
   -config <path to config file>  \
   -profile <name of profile>
 ```
@@ -265,7 +265,7 @@ 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 v0.4.1`, then you will want to set `-r v0.4.1` 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 v0.4.2`, then you will want to set `-r v0.4.2` for `get_refs.py` as well to be sure you have the correct containers.
 Be 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:

diff --git a/internal-instructions.md b/internal-instructions.md
@@ -21,7 +21,7 @@ nextflow run AlexsLemonade/scpca-nf -profile ccdl,batch
 When running the workflow for a project or group of samples that is ready to be released on ScPCA portal, please use the tag for the latest release:
 
 ```
-nextflow run AlexsLemonade/scpca-nf -r v0.4.1 -profile ccdl,batch --project SCPCP000000
+nextflow run AlexsLemonade/scpca-nf -r v0.4.2 -profile ccdl,batch --project SCPCP000000
 ```
 
 ### Processing example data

diff --git a/modules/af-features.nf b/modules/af-features.nf
@@ -9,8 +9,11 @@ process index_feature{
     tuple val(id), path("feature_index")
   script:
     """
+    # ensure salmon only gets the first 2 columns here
+    cut -f 1,2 ${feature_file} > feature_barcodes.txt
+
     salmon index \
-      -t ${feature_file} \
+      -t feature_barcodes.txt \
       -i feature_index \
       --features \
       -k 7

diff --git a/nextflow.config b/nextflow.config
@@ -5,7 +5,7 @@ manifest{
   homePage = 'https://github.com/AlexsLemonade/scpca-nf'
   mainScript = 'main.nf'
   defaultBranch = 'main'
-  version = 'v0.4.1'
+  version = 'v0.4.2'
 }
 
 // global parameters for workflows