Merge pull request #753 from AlexsLemonade/allyhawkins/example-data-h5ad

Fix bugs with generating example data

config/profile_example.config

@@ -4,6 +4,7 @@ params {
   run_metafile = "s3://scpca-references/example-data/example_run_metadata.tsv"
   sample_metafile = "s3://scpca-references/example-data/example_sample_metadata.tsv"
   project_celltype_metafile = "s3://scpca-references/example-data/example_project_celltype_metadata.tsv"
+  cellhash_pool_file = "s3://scpca-references/example-data/example_multiplex_pools.tsv"
 
   outdir = "s3://scpca-references/example-data/scpca_out"
 

internal-instructions.md

@@ -95,12 +95,13 @@ nextflow run AlexsLemonade/scpca-nf -r v0.8.1 -profile ccdl,batch --project SCPC
 We provide an [example of the expected outputs](./examples/README.md#example-output) after running `scpca-nf` available for external users.
 If there have been major updates to the directory structure or the contents of the output, the example data should be re-processed such that the example output we provide mimics the current expected output from `scpca-nf`.
 
-First, please check the metadata files present in `s3://scpca-references/example-data` are up to date with changes in the workflow.
+First, please check the metadata files present in `s3://scpca-references/example-data` are up to date with changes in the workflow and reflect the contents of the files present in the `examples` directory of this repository.
 Each of these files should be present, with the expected input columns as described in each documentation link.
 
 - `example_run_metadata.tsv` ([documentation](./external-instructions.md#prepare-the-run-metadata-file))
 - `example_sample_metadata.tsv` ([documentation](./external-instructions.md#prepare-the-sample-metadata-file))
 - `example_project_celltype_metadata.tsv` ([documentation](./external-instructions.md#preparing-the-project-cell-type-metadata-file))
+- `example_multiplex_pools.tsv` ([documentation](./external-instructions.md#multiplexed-cellhash-libraries))
 
 Once you have confirmed that the metadata looks correct, use the following commands to run the workflow and re-process the example data:
 

main.nf

@@ -69,7 +69,7 @@ if (!resolution_strategies.contains(params.af_resolution)) {
 }
 
 if (params.cellhash_pool_file && !file(params.cellhash_pool_file).exists()){
-  log.error("The 'cellhash_pool_file' file ${cellhash_pool_file} can not be found.")
+  log.error("The 'cellhash_pool_file' file ${params.cellhash_pool_file} can not be found.")
   param_error = true
 }