use project 1 and add file

AlexsLemonade · Jan 2, 2024 · 9ef62cf · 9ef62cf
1 parent d684ab7
commit 9ef62cf
Show file tree

Hide file tree

Showing 20 changed files with 13 additions and 3 deletions.
diff --git a/.github/workflows/nextflow-stub-check.yaml b/.github/workflows/nextflow-stub-check.yaml
@@ -31,7 +31,7 @@ jobs:
       - name: Check Nextflow workflow for merging objects
         uses: docker://nextflow/nextflow:21.10.6
         with:
-          args: nextflow -log merge-run.log run merge.nf -stub -profile stub -ansi-log false --project STUBP06
+          args: nextflow -log merge-run.log run merge.nf -stub -profile stub -ansi-log false --project STUBP01
 
       - name: Join log files
         if: ${{ !cancelled() }}

diff --git a/merge.nf b/merge.nf
@@ -146,7 +146,7 @@ workflow {
       .map{[
         it.scpca_project_id,
         it.scpca_library_id,
-        "${params.results_dir}/${it.scpca_project_id}/${it.scpca_sample_id}/${it.scpca_library_id}_processed.rds"
+        file("${params.results_dir}/${it.scpca_project_id}/${it.scpca_sample_id}/${it.scpca_library_id}_processed.rds")
       ]}
       // only include libraries that have been processed through scpca-nf
       .filter{file(it[2]).exists()}

diff --git a/test/.gitignore b/test/.gitignore
@@ -1 +1,8 @@
-output/
+output/checkpoints/
+output/results/STUBP02/
+output/results/STUBP03/
+output/results/STUBP04/
+output/results/STUBP05/
+output/results/STUBP06/
+output/results/STUBP07/
+output/results/STUBP08/
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_celltype-report.html b/test/output/results/STUBP01/STUBS01/STUBL01_celltype-report.html
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_filtered.rds b/test/output/results/STUBP01/STUBS01/STUBL01_filtered.rds
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_filtered_rna.hdf5 b/test/output/results/STUBP01/STUBS01/STUBL01_filtered_rna.hdf5
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_metadata.json b/test/output/results/STUBP01/STUBS01/STUBL01_metadata.json
@@ -0,0 +1 @@
+{"unfiltered_cells": 10, "filtered_cells": 10, "processed_cells": 10}
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_processed.rds b/test/output/results/STUBP01/STUBS01/STUBL01_processed.rds
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_processed_annotated.rds b/test/output/results/STUBP01/STUBS01/STUBL01_processed_annotated.rds
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_processed_rna.hdf5 b/test/output/results/STUBP01/STUBS01/STUBL01_processed_rna.hdf5
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_unfiltered.rds b/test/output/results/STUBP01/STUBS01/STUBL01_unfiltered.rds
diff --git a/test/output/results/STUBP01/STUBS01/STUBL01_unfiltered_rna.hdf5 b/test/output/results/STUBP01/STUBS01/STUBL01_unfiltered_rna.hdf5
diff --git a/test/output/results/STUBP01/STUBS16/STUBL16_filtered.rds b/test/output/results/STUBP01/STUBS16/STUBL16_filtered.rds
diff --git a/test/output/results/STUBP01/STUBS16/STUBL16_filtered_rna.hdf5 b/test/output/results/STUBP01/STUBS16/STUBL16_filtered_rna.hdf5
diff --git a/test/output/results/STUBP01/STUBS16/STUBL16_metadata.json b/test/output/results/STUBP01/STUBS16/STUBL16_metadata.json
@@ -0,0 +1 @@
+{"unfiltered_cells": 10, "filtered_cells": 10, "processed_cells": 10}
diff --git a/test/output/results/STUBP01/STUBS16/STUBL16_processed.rds b/test/output/results/STUBP01/STUBS16/STUBL16_processed.rds
diff --git a/test/output/results/STUBP01/STUBS16/STUBL16_processed_rna.hdf5 b/test/output/results/STUBP01/STUBS16/STUBL16_processed_rna.hdf5
diff --git a/test/output/results/STUBP01/STUBS16/STUBL16_unfiltered.rds b/test/output/results/STUBP01/STUBS16/STUBL16_unfiltered.rds
diff --git a/test/output/results/STUBP01/STUBS16/STUBL16_unfiltered_rna.hdf5 b/test/output/results/STUBP01/STUBS16/STUBL16_unfiltered_rna.hdf5
diff --git a/test/stub-run-metadata.tsv b/test/stub-run-metadata.tsv
@@ -14,3 +14,4 @@ STUBR12	STUBL11	STUBS12,STUBS13	STUBP06	10Xv3.1	cell	stub	test/runs/STUBR12	NA	N
 STUBR13	STUBL11	STUBS12,STUBS13	STUBP06	cellhash_10Xv3	cell	stub	test/runs/STUBR13	test/references/barcodes/cellhash.stub.tsv	2[1-15]	NA	NA	NA
 STUBR14	STUBL12	STUBS14	STUBP07	10Xv3.1	cell	stub	test/runs/STUBR14	NA	NA	NA	NA	test/celltypes/STUBL12-submitter-celltypes.tsv
 STUBR15	STUBL13	STUBS15	STUBP08	10Xv3.1	cell	stub	test/runs/STUBR15	NA	NA	NA	NA	NA
+STUBR16	STUBL16	STUBS16	STUBP01	10Xv2	cell	stub	test/runs/STUBR16	NA	NA	NA	NA	NA
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		{"unfiltered_cells": 10, "filtered_cells": 10, "processed_cells": 10}